| 09ce055 | Martin Cech | 30 August 2024, 17:31:37 UTC | add chainnet tool from ucsc/kent (#6284) | 30 August 2024, 17:31:37 UTC |
| 21578f9 | Rlibouban | 30 August 2024, 15:01:10 UTC | update BUSCO and fix --miniprot parameter (#6153) * update BUSCO and fiw --miniprot parameter * error version * update * fix miniprot parameter * update test-data * update * small modification on busco db * small modifications * fix output errors * small modification * small modification * fix test * add test-data/genome_results_miniprot * small change in busco.xml * update test-data * add assert * fix test 7 | 30 August 2024, 15:01:10 UTC |
| 3d970de | gxydevbot | 30 August 2024, 14:28:03 UTC | Updating tools/cami_amber from version 2.0.4 to 2.0.5 (#6266) * Updating tools/cami_amber from version 2.0.4 to 2.0.5 * Update tools/cami_amber/macros.xml --------- Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com> Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 30 August 2024, 14:28:03 UTC |
| 140ef12 | Lucille Delisle | 30 August 2024, 13:58:09 UTC | Fix _ Upgrade rna quast (#6288) * bump rnaQUAST version * fix STAR command check | 30 August 2024, 13:58:09 UTC |
| d68ebc9 | Lucille Delisle | 30 August 2024, 13:10:34 UTC | Fix RNAquast wrapper when identifiers have non \w characters (#6287) * rename second input file to test substitute characters * Fix cases where identifiers contains non regular characters * solve issue with dash in names * bump version suffix | 30 August 2024, 13:10:34 UTC |
| e3de8bc | Ross Lazarus | 30 August 2024, 10:08:59 UTC | Add filter by expression option to samtools_view (#6283) * Preparing draft PR * typo * typo * redundant copy * fix flakery * sheesh. local flake8 was fine, I swear.... * Add comments explaining two non-obvious issues being dealt with - 1 based reporting and decorated sorting for bed output * flake8 strikes again. * flake8 a trailing space. Oy. * added a native pytrf mode to run findstr and make csv or tsv or gtf format output for all perfect STRs. This makes the tool more generic and makes better use of pytrf... * update readme with stuff from the tool help * forgot the new test output for the new native pytrf findstr command line test * make native test output smaller than 43MB. Eeesh. * add missing smaller test fa * remove bogus print * Add test for built-in genome and paraphenaliae * reverted the inbuilt test because cannot get the output labelled informatively about the provenance otherwise. Cannot pass the element_identifier from a test parameter it seems - it's a built-in so not surprisingly over-ridden. * rationalise minima for everything. fix dimer minimum of 1 fix tests to conform to new structures * make bed sample small enough * add option for windowed density bigwig output with selectable window size for size selected and specified motifs not so easy for native pytrf operation * fix flake8 issue * more flakery * remove pybigtools to use ucsc-bedgraphtobigwig on a bedgraph instead jbrowse2 simply will not read the bigwigs made using pybigtools :( * Fixes suggested by Bjoern's review * Update tools/microsatbed/microsatbed.xml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Update microsatbed.xml * add help for windowed density bigwig option * fix logic for multiple flags add contents assertions to all tests * remove bogus old merge mark * remove unusual version tokens broken by update bot. * remove unused tokens * Fix indexed genome Update some text and help * add built in genome test * Better to know what the input was * test indexed genome in the last test * try on_string for label as source * bump version suffix * Update samtools to 1.20; add option to filter on an expression such as sclen>300; and a new test * forgot to save macros with new version :( * update test data after version bump * revert to samtools 1.15.1 as 1.20 seems to break some other samtools tools * update tests to 1.15.1 to see if other tools now also pass tests * Update samtools_view.xml to delta=500 * Update samtools_view.xml * transfer changes from the draft PR - add help for filter expressions and a separate version string for samtools_view * forgot the new test output bam :( * Update tool_collections/samtools/samtools_view/samtools_view.xml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Update tool_collections/samtools/samtools_view/samtools_view.xml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Update tool_collections/samtools/samtools_view/samtools_view.xml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * fix duplicate ftypes :) * update tests after some suggested changes --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 30 August 2024, 10:08:59 UTC |
| 93fe734 | Björn Grüning | 29 August 2024, 10:10:08 UTC | meme updates (#6275) * meme updates * fix lints * convert tests to asserts | 29 August 2024, 10:10:08 UTC |
| cc4c7a0 | Hugo Lefeuvre | 28 August 2024, 20:13:19 UTC | Add tool argNorm (#6282) * Add argNorm + test files * Rename .shed.yml * Update tools/argnorm/argnorm.xml Add argument instead of name Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Update tools/argnorm/argnorm.xml Add argument instead of name Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Update tools/argnorm/argnorm.xml Add argument instead of name Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Update tools/argnorm/argnorm.xml Add argument instead of name Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Update tools/argnorm/argnorm.xml Add argument instead of name Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * remove xref * Added xref since the tool was added to biotools --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 28 August 2024, 20:13:19 UTC |
| 10aeeb4 | Boris Depoortere | 28 August 2024, 12:42:23 UTC | Added Astral (#6271) * Added Astral * Updates to linting with flake8 * changes after feedback * R script can be deleted, cfr. https://github.com/smirarab/ASTRAL/blob/master/astral-tutorial.md#file-export-of-branch-annotations * deletion of file as bootstrapping is not a wrapper option (less reliable: https://github.com/smirarab/ASTRAL/blob/master/astral-tutorial.md#multi-locus-bootstrapping) * removed unnecessary files --------- Co-authored-by: boris.depoortere <boris.depoortere@vib.be> | 28 August 2024, 12:42:23 UTC |
| 2b3fa63 | Marius van den Beek | 27 August 2024, 13:53:00 UTC | Merge pull request #6169 from bgruening/star_wasp Add WASP mode to STAR as requested by a user | 27 August 2024, 13:53:00 UTC |
| 6770266 | Pablo Moreno | 27 August 2024, 12:59:34 UTC | Update InferCNV: control number of threads, downgrade profile and sparse matrix support (#6263) * InferCNV control number of threads and downgrade profile * Bump suffix, downgrade profile * Change way in which we access GALAXY_SLOTS * Lets see if these are the offending changes * ...missing something * Another variant based on callvariants.xml * Grab GALAXY_SLOTS from R * avoid arrow assignments * make sure threads come as numeric * Test data for sparse matrix loading * Additional logic for 10x and test * Further fixes and docs. * Make life easier when using this in the UI * Apply suggestions from code review Co-authored-by: Amirhossein <66441226+nilchia@users.noreply.github.com> * Remove tsv, allow txt --------- Co-authored-by: Amirhossein <66441226+nilchia@users.noreply.github.com> | 27 August 2024, 12:59:34 UTC |
| c04516d | Bjoern Gruening | 27 August 2024, 10:46:19 UTC | fix test | 27 August 2024, 11:52:56 UTC |
| e5089a1 | Bjoern Gruening | 27 August 2024, 10:46:05 UTC | add new VCF file from @mthang | 27 August 2024, 11:52:56 UTC |
| 7ab4dc5 | Björn Grüning | 26 August 2024, 17:21:20 UTC | Update tools/rgrnastar/rg_rnaStar.xml | 27 August 2024, 11:52:56 UTC |
| 61f7214 | Björn Grüning | 01 August 2024, 15:28:42 UTC | Update rg_rnaStar.xml | 27 August 2024, 11:52:56 UTC |
| 7120e14 | Björn Grüning | 01 August 2024, 15:18:48 UTC | add an option to overwrite GALAXY_STAR_LIMIT_GENOME_GENERATE_RAM for admins | 27 August 2024, 11:52:56 UTC |
| ff9db95 | Bjoern Gruening | 22 July 2024, 17:07:43 UTC | use macros for wasp, it also works for star_solo | 27 August 2024, 11:52:56 UTC |
| dc44568 | Bjoern Gruening | 22 July 2024, 16:45:40 UTC | include varVCF | 27 August 2024, 11:52:56 UTC |
| d6679c6 | Martin Cech | 27 August 2024, 10:17:13 UTC | add chainprenet tool from ucsc/kent (#6251) * add chainprenet tool from ucsc/kent standardise tool ids Co-authored-by: Björn Grüning <bjoern@gruenings.eu> synx folder name and tool id * drop useless param and fix text minimize test data, exercise data table * Apply suggestions from code review --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 27 August 2024, 10:17:13 UTC |
| cd59ba2 | Saim Momin | 27 August 2024, 10:01:23 UTC | Updated test parameters for tools/bbtools (#6281) * Updating tools/bbtools from version 39.06 to 39.08 * fixing test and reformating * Fixed test parameters --------- Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com> Co-authored-by: Bjoern Gruening <bjoern.gruening@gmail.com> | 27 August 2024, 10:01:23 UTC |
| 329ba03 | Martin Cech | 27 August 2024, 07:22:38 UTC | add UCSC's axt to MAF converter (#6199) * add UCSC's axt to maf converter * allow selecting fasta indexes from data tables match folder name and tool id * add data table test, cleanup * Apply suggestions from code review --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 27 August 2024, 07:22:38 UTC |
| 8f49573 | Polina Polunina | 26 August 2024, 18:03:48 UTC | VirHEAT: fix error when no .vcf in samplename (#6103) * fix error when no .vcf in samplename * add configfile * update wrapper version * add -r param to update to 0.7.1 * fix command * Update tools/virheat/macros.xml --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 26 August 2024, 18:03:48 UTC |
| b20df95 | Martin Cech | 26 August 2024, 17:24:45 UTC | add axtchain tool from ucsc (#6243) minify test data by using mitochondria match folder name and tool id fix param passing | 26 August 2024, 17:24:45 UTC |
| cb30e4b | gxydevbot | 26 August 2024, 16:08:30 UTC | Updating tools/ampvis2 from version 2.8.6 to 2.8.9 (#6277) * Updating tools/ampvis2 from version 2.8.6 to 2.8.9 * adapt asserts * add delta to have a bit more freedom in the text * Update alpha_diversity.xml * Update alpha_diversity.xml --------- Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com> Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 26 August 2024, 16:08:30 UTC |
| 606882f | Björn Grüning | 26 August 2024, 15:25:20 UTC | Update ncbi-gtdb_map.xml (#6279) | 26 August 2024, 15:25:20 UTC |
| 7632986 | Saim Momin | 26 August 2024, 14:41:48 UTC | Fixing test data for fastq_dump and fasterq_dump tool updation PR #6123 (#6260) * Update fastq_dump.xml * Update fasterq_dump.xml * Updated test data for fastq_dump * fasterq_dump test fix * test data update * Re-trying updating the test-data * Retrying updating test data * Updated test of fastq dump * Updated fasterq_dump * bump --------- Co-authored-by: Diego De Panis <9466288+diegomics@users.noreply.github.com> Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 26 August 2024, 14:41:48 UTC |
| 976ad08 | Martin Cech | 26 August 2024, 13:48:01 UTC | add chainsort from ucsc/kent (#6252) standardise tool id, simplify params Co-authored-by: Björn Grüning <bjoern@gruenings.eu> fix test match folder name and tool id match folder and tool id | 26 August 2024, 13:48:01 UTC |
| faa8c4b | gxydevbot | 26 August 2024, 13:40:17 UTC | Updating tools/adapter_removal from version 2.3.3 to 2.3.4 (#6276) * Updating tools/adapter_removal from version 2.3.3 to 2.3.4 * add the new 2 parameters --------- Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com> Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 26 August 2024, 13:40:17 UTC |
| af516fb | Björn Grüning | 25 August 2024, 15:23:00 UTC | Update .shed.yml | 25 August 2024, 15:23:00 UTC |
| 5b1dd77 | SantaMcCloud | 25 August 2024, 14:47:44 UTC | Add Gtdb to taxdump (#6148) * Add name2taxid function from taxonkit * rename file * rename file * rename file and change a param * a little fix * Add gtdb_to_taxdump * little fix * a commit do restart the tests * fix test with column error * fix tests * remove takonkit commits from this branche * fix test such that they have an output * fix test file size * added the dm option but doesnt work yet * dm now working * Update ncbi-gtdb_map.xml * add biotools id * add version column * add the note to look at the help section * change for new DM * change DM * Update tools/gtdb_to_taxdump/ncbi-gtdb_map.xml Co-authored-by: paulzierep <paul.zierep@googlemail.com> * Update tools/gtdb_to_taxdump/ncbi-gtdb_map.xml Co-authored-by: paulzierep <paul.zierep@googlemail.com> * Update tools/gtdb_to_taxdump/ncbi-gtdb_map.xml Co-authored-by: paulzierep <paul.zierep@googlemail.com> * now the test works fine with the dm at least now! * maybe no it is clear? * fix typo in the file names * fix typo in the file names * change to wildcards * Update tool_data_table_conf.xml.sample * Apply suggestions from code review * Update tools/gtdb_to_taxdump/tool-data/gtdbtk_database_metadata_versioned.loc.sample --------- Co-authored-by: paulzierep <paul.zierep@googlemail.com> Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 25 August 2024, 14:47:44 UTC |
| df3de3f | Björn Grüning | 25 August 2024, 14:36:21 UTC | fix shed.yml lint warning (#6274) | 25 August 2024, 14:36:21 UTC |
| 02d2f93 | M Bernt | 25 August 2024, 14:18:05 UTC | Fix all flake8 linter problems (#6189) * fix flake8 linter problems * one more | 25 August 2024, 14:18:05 UTC |
| a773446 | heylf | 25 August 2024, 13:10:13 UTC | Add Spapros (#6191) * add evaluation.xml * first version of macros.xml * first version of shed.yml * adding second test to evaluation * finished evaluation tool, ready for review * Changes to shed.yml * some fixes and code improvements for evaluatio.xml * fix typo in macros.xml * Adding selection.xml for spapros selction * adding test data for spapros * change to 240cells data evaluation.xml * changes to selection.xml to optimize tests * optimize test data * Review changed to evaluation.xml * Review changes to macros.xml * Review changes to selection.xml * adding image asserts * Update tools/spapros/selection.xml * Update selection.xml * synthax fix selection.xml * bugfix selection.xml * changes to marker_out_test4.tsv * solving issue with line switches of marker files * fix to slection.xml tests * changes to ci and pr yaml to take tifffile into account * Revert "changes to ci and pr yaml to take tifffile into account" This reverts commit 1b71a0973a09f3d281ecdf91cebdd283f32ed572. * remove file comparisions * rsolve merge conflict for selection.xml * resolve assert for evaluation.xml * remove pngs * bugfix selection.xml * updating marker_out.tsvs * fixing image differnece for slection.xml * fixing image differnece for slection.xml * fix typo * figuring out reproducibility isse * Try to fix reproducibility issue * Try to fix reproducibility issue * Try to fix reproducibility issue * Try to fix reproducibility issue * figureing out what is going on * figureing out what is going on --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 25 August 2024, 13:10:13 UTC |
| 91090b1 | SantaMcCloud | 25 August 2024, 13:05:22 UTC | Add CAMI amber uitltiy script (#6268) * Add name2taxid function from taxonkit * rename file * rename file * rename file and change a param * a little fix * Add gtdb_to_taxdump * little fix * a commit do restart the tests * fix test with column error * fix tests * remove takonkit commits from this branche * fix test such that they have an output * fix test file size * added the dm option but doesnt work yet * dm now working * Update ncbi-gtdb_map.xml * add biotools id * add version column * add the note to look at the help section * change for new DM * change DM * Update tools/gtdb_to_taxdump/ncbi-gtdb_map.xml Co-authored-by: paulzierep <paul.zierep@googlemail.com> * Update tools/gtdb_to_taxdump/ncbi-gtdb_map.xml Co-authored-by: paulzierep <paul.zierep@googlemail.com> * Update tools/gtdb_to_taxdump/ncbi-gtdb_map.xml Co-authored-by: paulzierep <paul.zierep@googlemail.com> * now the test works fine with the dm at least now! * maybe no it is clear? * fix typo in the file names * fix typo in the file names * change to wildcards * Add a utility script for CAMI amber * remove commit form different branch * change macros * Update tools/cami_amber/biobox_add_taxid.xml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * cahnge the way of ln files * cahnge the way of cp file * change var name to output * change column type to data_column * Commit to start the test again * fix a little typo * fix test * delete unnecessary code * remove softlinks since they are not needed * make the interface userfrindly * fix help text --------- Co-authored-by: paulzierep <paul.zierep@googlemail.com> Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 25 August 2024, 13:05:22 UTC |
| 7f32f58 | richard-burhans | 23 August 2024, 20:44:28 UTC | updating ncbi fcs-gx to version 0.5.4 (#6273) * updating ncbi fcs-gx to version 0.5.4 * updating test data --------- Co-authored-by: Richard C. Burhans <rico@bx.psu.edu> | 23 August 2024, 20:44:28 UTC |
| 3234c3d | planemo-autoupdate | 23 August 2024, 08:07:36 UTC | Updating tools/dram from version 1.3.5 to 1.5.0 (#4998) * Updating tools/dram from version 1.3.5 to 1.5.0 * fix one test * make tests pass --------- Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com> Co-authored-by: Bjoern Gruening <bjoern.gruening@gmail.com> | 23 August 2024, 08:07:36 UTC |
| 81d7b9e | gxydevbot | 22 August 2024, 18:37:36 UTC | Updating tools/tracegroomer from version 0.1.3 to 0.1.4 (#6226) Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com> | 22 August 2024, 18:37:36 UTC |
| f5a9be9 | planemo-autoupdate | 22 August 2024, 17:37:12 UTC | Updating tools/cemitool from version 1.18.1 to 1.26.0 (#4922) Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com> | 22 August 2024, 17:37:12 UTC |
| 06a9256 | Björn Grüning | 22 August 2024, 08:06:57 UTC | add new functions from the python math module (#6258) * add new functions from the python math module * Update .shed.yml * Update tools/column_maker/column_maker.xml Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> * latest updates * fix linting * remove e * update test data --------- Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 22 August 2024, 08:06:57 UTC |
| ab5e118 | Marie LEFEBVRE | 21 August 2024, 13:02:15 UTC | Fix blast2tsv module (#6241) * Fix blast2tsv module * Fix flake8 warning * Add fstring * Add again xref bio.tools * Fix blast2tsv tests * Fix rps2tsv tests * Fix lint * Add more specificity to tests * Expand xrefs * Change tsv to tabular * Update virAnnot_otu.xml * Update virAnnot_rps2tsv.xml --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 21 August 2024, 13:02:15 UTC |
| 3c21a75 | Marius van den Beek | 21 August 2024, 07:41:39 UTC | Revert "ci.yaml and pr.yaml update (#6218)" (#6228) This reverts commit 30843d2e3fd504a29c09e8b28229572810c9db25. | 21 August 2024, 07:41:39 UTC |
| b01085b | Nate Coraor | 21 August 2024, 07:27:34 UTC | Small ColabFold updates (#6261) * Add env var to colabfold_msa to allow admins to set extra params (such as `--host-url`) * Multiple a3m outputs for colabfold_alphafold * Bump colabfold_* galaxy version | 21 August 2024, 07:27:34 UTC |
| 0ef475d | heylf | 20 August 2024, 09:22:07 UTC | Scanpy plot new function (#6113) * update macros * update plot.xml * add test data * Adding test data * small change to filter.xml * Update tools/scanpy/macros.xml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 20 August 2024, 09:22:07 UTC |
| fce5664 | pvanheus | 20 August 2024, 08:32:17 UTC | Update iqtree and fix some options (#6259) | 20 August 2024, 08:32:17 UTC |
| cafe2a4 | Khaled196 | 19 August 2024, 16:34:37 UTC | fix text in cnv.xml (#6257) | 19 August 2024, 16:34:37 UTC |
| 65b5c6f | Wolfgang Maier | 19 August 2024, 15:24:14 UTC | Add masking of small clusters and parsing of different input flavors to new hierarchical clustering tool (#6255) * Add option to mask assignments to clusters smaller than a given size * Add test dataset * Parse different input flavors This adds parsing of inputs without column or row names * Expand macro in n_cluster branch * Use rstrip instead of strip consistently where possible | 19 August 2024, 15:24:14 UTC |
| 23f6d9e | Khaled196 | 19 August 2024, 10:40:20 UTC | update cnv tool and forward the test to test collection (#6250) * update cnv tool and forward the test to test collection * fix version | 19 August 2024, 10:40:20 UTC |
| 90f5b1b | Helge Hecht | 19 August 2024, 10:38:35 UTC | added beta parameter to cemitool (#6247) * added beta parameter * added version suffix * renamed param to beta * made beta parameter optional * removed default value * Update tools/cemitool/cemitool.xml --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 19 August 2024, 10:38:35 UTC |
| 6b50408 | gxydevbot | 19 August 2024, 06:39:03 UTC | Updating tools/prot-scriber from version 0.1.5 to 0.1.6 (#6254) Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com> | 19 August 2024, 06:39:03 UTC |
| 784611c | Marius van den Beek | 16 August 2024, 13:12:20 UTC | Merge pull request #6249 from mvdbeek/bcftools_call Fix bcftools cheetah section variable name | 16 August 2024, 13:12:20 UTC |
| 80b48ca | mvdbeek | 16 August 2024, 11:18:50 UTC | Touch files that use macro | 16 August 2024, 11:18:50 UTC |
| d6831a8 | mvdbeek | 16 August 2024, 11:04:34 UTC | Fix cheetah section variable name There's no tgts_secion defined anywhere in the bcftools wrappers. | 16 August 2024, 11:04:42 UTC |
| 05ce3d2 | Saim Momin | 16 August 2024, 08:52:05 UTC | Updated test data for nanoplot (#6248) * Updating tools/nanoplot from version 1.42.0 to 1.43.0 * Updated test data --------- Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com> | 16 August 2024, 08:52:05 UTC |
| 0bb6200 | paulzierep | 16 August 2024, 08:35:10 UTC | update (#6244) | 16 August 2024, 08:35:10 UTC |
| 9ed0c30 | paulzierep | 16 August 2024, 08:34:39 UTC | Fix ampvis2 NA in metadata error (#6213) * fix NA * bump version * added test and improved the fix | 16 August 2024, 08:34:39 UTC |
| 5607ad5 | Björn Grüning | 15 August 2024, 13:25:53 UTC | Taxonkit (#6245) * fix sample data and sample tests * fix tests | 15 August 2024, 13:25:53 UTC |
| 048d285 | Bjoern Gruening | 14 August 2024, 19:38:55 UTC | remove test file | 14 August 2024, 19:38:55 UTC |
| 703018a | SantaMcCloud | 14 August 2024, 17:52:42 UTC | Add name2taxid function from taxonkit (#6146) * Add name2taxid function from taxonkit * rename file * rename file * rename file and change a param * a little fix * change the test such that files will be compared * make the name options a bit clear * did an example for the show rank option * Update tools/taxonkit/taxonkit_name2taxid.xml Co-authored-by: paulzierep <paul.zierep@googlemail.com> * Update tools/taxonkit/taxonkit_name2taxid.xml Co-authored-by: paulzierep <paul.zierep@googlemail.com> * Update tools/taxonkit/taxonkit_name2taxid.xml Co-authored-by: paulzierep <paul.zierep@googlemail.com> * Update tools/taxonkit/taxonkit_name2taxid.xml Co-authored-by: paulzierep <paul.zierep@googlemail.com> * test for fix * test commit * fix test * fix test * commit to fix format problems * Update taxonkit_name2taxid.xml The format was not boken on my side so i try to fix in here in GitHub now. I hope this is better now * format fix maybe * delet file for reseting it on github * add the deleted file to see if the format is fixes now * Update taxonkit_name2taxid.xml ... maybe now the format is fixed * foramted * Update tools/taxonkit/taxonkit_name2taxid.xml * change such that the newest version will be dowanloaded and unpacked for the user * change but fomrat problem * fix file format * Apply suggestions from code review * Delete tools/taxonkit/test-data/test-db/names.dmp * Delete tools/taxonkit/test-data/test-db/delnodes.dmp * Update tools/taxonkit/taxonkit_name2taxid.xml Co-authored-by: paulzierep <paul.zierep@googlemail.com> * Update tools/taxonkit/taxonkit_name2taxid.xml Co-authored-by: paulzierep <paul.zierep@googlemail.com> * revert deleting * change value names * fix test * now fixed --------- Co-authored-by: paulzierep <paul.zierep@googlemail.com> Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 14 August 2024, 17:52:42 UTC |
| 9f0b54a | SantaMcCloud | 14 August 2024, 17:51:55 UTC | change the url to the right files (#6242) | 14 August 2024, 17:51:55 UTC |
| 868f438 | Marius van den Beek | 14 August 2024, 15:36:56 UTC | Fix bcftools call templating error (#6238) * Fix bcftools call Fixes https://github.com/galaxyproject/tools-iuc/issues/6177 * Add bcftools call test for target file option This test would previously resulted in a cheetah templating error. | 14 August 2024, 15:36:56 UTC |
| b890cd8 | Saim Momin | 14 August 2024, 15:34:53 UTC | Updating LUCA database version in Omamer data manager (#6237) * Updating LUCA database version in Omamer data manager * Added more options for database * Updated minor change in test * Version bump * Updated database list | 14 August 2024, 15:34:53 UTC |
| 0c8ab2d | Ross Lazarus | 14 August 2024, 08:41:26 UTC | fix for inbuilt genomes as input to microsatbed (#6232) * Preparing draft PR * typo * typo * redundant copy * fix flakery * sheesh. local flake8 was fine, I swear.... * Add comments explaining two non-obvious issues being dealt with - 1 based reporting and decorated sorting for bed output * flake8 strikes again. * flake8 a trailing space. Oy. * added a native pytrf mode to run findstr and make csv or tsv or gtf format output for all perfect STRs. This makes the tool more generic and makes better use of pytrf... * update readme with stuff from the tool help * forgot the new test output for the new native pytrf findstr command line test * make native test output smaller than 43MB. Eeesh. * add missing smaller test fa * remove bogus print * Add test for built-in genome and paraphenaliae * reverted the inbuilt test because cannot get the output labelled informatively about the provenance otherwise. Cannot pass the element_identifier from a test parameter it seems - it's a built-in so not surprisingly over-ridden. * rationalise minima for everything. fix dimer minimum of 1 fix tests to conform to new structures * make bed sample small enough * add option for windowed density bigwig output with selectable window size for size selected and specified motifs not so easy for native pytrf operation * fix flake8 issue * more flakery * remove pybigtools to use ucsc-bedgraphtobigwig on a bedgraph instead jbrowse2 simply will not read the bigwigs made using pybigtools :( * Fixes suggested by Bjoern's review * Update tools/microsatbed/microsatbed.xml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Update microsatbed.xml * add help for windowed density bigwig option * fix logic for multiple flags add contents assertions to all tests * remove bogus old merge mark * remove unusual version tokens broken by update bot. * remove unused tokens * Fix indexed genome Update some text and help * add built in genome test * Better to know what the input was * test indexed genome in the last test * try on_string for label as source * bump version suffix --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 14 August 2024, 08:41:26 UTC |
| ad14947 | paulzierep | 13 August 2024, 21:04:00 UTC | Update GTDB-TK DM (#6234) * update gtdb-tk DM * fix hidden * fix hidden * Update data_managers/data_manager_gtdbtk_database_installer/data_manager/gtdbtk_database_installer.xml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * add help * Apply suggestions from code review Its not a boolean anymore. Its type=hidden * Rename gtdbtk_database_versioned.loc to gtdbtk_database_versioned.loc.sample --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 13 August 2024, 21:04:00 UTC |
| 4290547 | BertBog | 13 August 2024, 13:22:01 UTC | Add PACU SNP phylogeny workflow (#6194) * Initial commit for PACU * Added the wrapper for the main PACU script * Updated PACU version to v0.0.4, switched to argument wherever possible * Addressed code review comments * Added missing profile * Switched /scratch/bebog/pacu_iuc/tools-iuc/tools/pacu to add the working directory * Updated version to v0.0.5 * Addressed code review comments | 13 August 2024, 13:22:01 UTC |
| 6b8fbd9 | Rand Zoabi | 13 August 2024, 11:36:12 UTC | Update fastp wrapper (#6231) * add --detect_adapter_forr_pe as a bool trimming option * remove redundant name | 13 August 2024, 11:36:12 UTC |
| f8c32a3 | Saim Momin | 13 August 2024, 11:35:38 UTC | Fixed minor linting issue in picrust2 (#6233) * Updating tools/picrust2 from version 2.5.1 to 2.5.3 * Fixed minor linting issue in test --------- Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com> | 13 August 2024, 11:35:38 UTC |
| c142110 | Björn Grüning | 12 August 2024, 07:06:10 UTC | udpate, fix pear (#6217) * udpate, fix pear * fix shed.yml * Update tools/pear/pear.xml * Apply suggestions from code review Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> --------- Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> | 12 August 2024, 07:06:10 UTC |
| 8a0f309 | Björn Grüning | 11 August 2024, 21:00:08 UTC | add explicit gbk suffix (#6223) | 11 August 2024, 21:00:08 UTC |
| 49a2861 | Björn Grüning | 11 August 2024, 20:59:30 UTC | add new reference genomes (#6221) | 11 August 2024, 20:59:30 UTC |
| 5b9441b | Björn Grüning | 11 August 2024, 20:58:58 UTC | fix for 6204 (#6216) | 11 August 2024, 20:58:58 UTC |
| 671a5fc | Björn Grüning | 11 August 2024, 20:20:09 UTC | add explicit connection type (#6215) * add explicit connection type * reformat | 11 August 2024, 20:20:09 UTC |
| 2652aac | Björn Grüning | 11 August 2024, 20:19:31 UTC | add -z option (#6222) | 11 August 2024, 20:19:31 UTC |
| 24d5739 | Björn Grüning | 11 August 2024, 20:18:41 UTC | add profiles to goenrichment (#6220) | 11 August 2024, 20:18:41 UTC |
| 30843d2 | heylf | 11 August 2024, 20:16:06 UTC | ci.yaml and pr.yaml update (#6218) * update ci.yaml * update pr.yaml * forget - | 11 August 2024, 20:16:06 UTC |
| a34052b | Wolfgang Maier | 08 August 2024, 19:18:57 UTC | Add new hierachical clustering tool based on scipy (#6214) * Add new hierachical clustering tool * Describe input format in tool help * Add .shed.yml * Add edam information * Fix flake8 issues * Add note about test data origin * Try to fix tests * Update tools/clustering_from_distmat/.shed.yml * Write column names to cluster assignment output --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 08 August 2024, 19:18:57 UTC |
| 6da96d8 | johaGL | 06 August 2024, 17:17:47 UTC | Metabologram fix (#6210) * update(metabologram): add user output option 'show_values' to write the values in the plots or not * metabologram: deleted metabolites selector as is not pertinent * input explanation: only abundances and mean enrichment accepted; improved Help text * metabologram: lint error solved, also more improvement of Help * update macros dimet: citation and suffix version; also for differential analysis improved Help * Update tools/dimet/macros.xml --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 06 August 2024, 17:17:47 UTC |
| cd51396 | M Bernt | 06 August 2024, 05:58:12 UTC | fastqc: set tmpdir (#6207) * fastqc: set tmpdir xref https://github.com/galaxyproject/galaxy/pull/18628 * Update tools/fastqc/rgFastQC.xml Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> --------- Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> | 06 August 2024, 05:58:12 UTC |
| d8a42fc | Rand Zoabi | 05 August 2024, 08:12:38 UTC | deprecate ebi_metagenomics_run_downloader (#6202) | 05 August 2024, 08:12:38 UTC |
| 0d2b1b7 | Saim Momin | 02 August 2024, 15:24:46 UTC | Updated tool to latest version and test-data (#6203) | 02 August 2024, 15:24:46 UTC |
| b57c22b | mthang | 01 August 2024, 12:22:47 UTC | patch combined_kreports.xml (#6182) * patch combined_kreports.xml * insert assert_contents into test 3 * use asserts for combine_kreports.xml * Update combine_kreports.xml --------- Co-authored-by: mthang <mthang@qfab.org> Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 01 August 2024, 12:22:47 UTC |
| 270d2e7 | Tom Harrop | 01 August 2024, 11:32:14 UTC | Update salsa2 for omnic (#6197) * fix typo * update tests * format * fix agp issue... maybe * fix agp issue... maybe * nasty hack for AGP :( * Update tools/salsa2/salsa2.xml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * awk comment --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 01 August 2024, 11:32:14 UTC |
| c21958f | Amirhossein | 31 July 2024, 17:37:53 UTC | Update inspect.xml (#6198) * Update inspect.xml * Update tools/scanpy/inspect.xml Co-authored-by: Pavankumar Videm <pavanvidem@gmail.com> * bump gx version * add test for percent_top) --------- Co-authored-by: Pavankumar Videm <pavanvidem@gmail.com> | 31 July 2024, 17:37:53 UTC |
| f12613b | Martin Cech | 31 July 2024, 14:15:12 UTC | Merge pull request #6196 from martenson/ucsc-maftoaxt add UCSC's maftoaxt converter/extractor | 31 July 2024, 14:15:12 UTC |
| df500c2 | Rand Zoabi | 30 July 2024, 15:10:34 UTC | Add bulk_download to mg_toolkit suite (#6190) * update .shed.yml * Add bulk_download to mg_toolkit suite * fix lint WARNINGs + review adjustments | 30 July 2024, 15:10:34 UTC |
| 768a604 | Martin Cech | 30 July 2024, 14:19:50 UTC | add quotes | 30 July 2024, 14:19:50 UTC |
| fa0f3ca | pvanheus | 30 July 2024, 14:12:19 UTC | Update clair3 (#6195) * Update clair3 to version 1.0.8 * Fix permissions * Increase lines_diff, bump profile * Really set lines_diff to 4 | 30 July 2024, 14:12:19 UTC |
| 4430dac | Martin Cech | 30 July 2024, 13:05:28 UTC | add long_description shed field | 30 July 2024, 13:05:28 UTC |
| 0f04160 | Martin Cech | 30 July 2024, 12:22:00 UTC | add UCSC's maftoaxt converter/extractor | 30 July 2024, 12:22:00 UTC |
| 9af8730 | gxydevbot | 29 July 2024, 07:17:40 UTC | Updating tools/bracken from version 2.9 to 3.0 (#6185) Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com> | 29 July 2024, 07:17:40 UTC |
| 3c1a0c4 | M Bernt | 29 July 2024, 07:01:55 UTC | Bump metaphlan (#6183) * Updating tools/metaphlan from version 4.0.6 to 4.1.0 * Updating tools/metaphlan from version 4.1.0 to 4.1.1 * add vsc arguments and use --offline using `--offline` is probably a good idea since otherwise metaphlan will download the latest reference DB (if no correct one is given, e.g. if the data table is misconfigured). * simplify metaphlan data manager * implement subsampling * fix datamanager test * fix tool test * Fix typo Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * add missing quotes * rename test loc files * add paired collection * reenable tests --------- Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com> Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 29 July 2024, 07:01:55 UTC |
| 1f7b04d | gxydevbot | 29 July 2024, 07:00:52 UTC | Updating tools/ncbi_entrez_direct from version 22.1 to 22.4 (#6186) Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com> | 29 July 2024, 07:00:52 UTC |
| 42b2d78 | gxydevbot | 29 July 2024, 06:48:37 UTC | Updating tools/recentrifuge from version 1.14.0 to 1.14.1 (#6187) Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com> | 29 July 2024, 06:48:37 UTC |
| f05d53e | gxydevbot | 29 July 2024, 06:47:43 UTC | Updating tools/unicycler from version 0.5.0 to 0.5.1 (#6188) Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com> | 29 July 2024, 06:47:43 UTC |
| 695ea58 | Albert Ber | 26 July 2024, 09:11:12 UTC | Added the profile2cami tool, a component of the TaxonKit suite. (#6085) * Added the profile2cami tool, a component of the TaxonKit suite. * Renamed shed.yml -> .shed.yml * Shrinked delnodes.dmp 684kb -> 150kb * Renamed test.loc -> ncbi_taxonomy.loc * Adjusted taxonkit, removed folder profile2cami, added suite in .shed.yml * Updated Taxonkit to version 0.17.0 - worked on issues. * Renamed taxonomy.loc -> taxonomy.loc.test * Adjusted test, adjusted loc.sample * Try to fix linting error * Resolving linting error * Adjusted the output label. | 26 July 2024, 09:11:12 UTC |
| 3cce4c7 | Ross Lazarus | 25 July 2024, 06:53:10 UTC | Add bigwig value ascii histogram and extreme value counts to optional bigwig outlier report (#6179) * adding new tool bigwig_outlier_bed * remove redundant script * replace test.bw with test-data/1.bigwig to decrease test outputs below 1MB maximum for linter. * added bigtools to bio.tools for this new entry added edam * Add a proper version command by importing pybedtools * fix doi for pybigtools * Incorporate Bjoern's ideas. Single select to configure 3 possible outputs. Upper quantile now required. Chide if no low quantile and no output because low not in the choice. Help vastly expanded. * Added the bigwig metadata name as the label for bed feature name so no need for the user to supply one. * Clearing out old test data. Passes tests here but diffs in CI. Something odd. * readding fixed test outputs again again. * Ah. was overwriting a bed with the two bigwig test. * remove print leftovers * Separated python script to enable access for linting in CI * fix flake8 complaints with black on the new separate python script * fix imports * Do not make the output contig statistics table if there's no table output needed. * make the table calculations optional and mostly as a separate function since they may not be needed. * Clean up some comments. makeTableRow renamed * Update tools/bigwig_outlier_bed/.shed.yml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Update tools/bigwig_outlier_bed/.shed.yml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Clean up all field prompt text and consolidate the help text into chunks. * remove test for both qhi/qlo because qhi is not optional * fix broken qlo parameter passing and tests - add test for no qlo. * Flake fix * update to 0.2.0 pybigtools test outputs are different :( * add ascii histogram and table of descriptive stats to tableout * fixes to tableout * clean up table output * update readme * add test and option to only produce table - no bed so faster. extend tool version string * typo * update tests to add bigwig label to histogram rows * fix flake * fix test outputs * remove non-standard version token to avoid update bot failure --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 25 July 2024, 06:53:10 UTC |
| 4f8728c | Ross Lazarus | 25 July 2024, 05:55:37 UTC | Update tool version and remove update-bot breaking non-standard version tokens from Microsatbed (#6181) * Preparing draft PR * typo * typo * redundant copy * fix flakery * sheesh. local flake8 was fine, I swear.... * Add comments explaining two non-obvious issues being dealt with - 1 based reporting and decorated sorting for bed output * flake8 strikes again. * flake8 a trailing space. Oy. * added a native pytrf mode to run findstr and make csv or tsv or gtf format output for all perfect STRs. This makes the tool more generic and makes better use of pytrf... * update readme with stuff from the tool help * forgot the new test output for the new native pytrf findstr command line test * make native test output smaller than 43MB. Eeesh. * add missing smaller test fa * remove bogus print * Add test for built-in genome and paraphenaliae * reverted the inbuilt test because cannot get the output labelled informatively about the provenance otherwise. Cannot pass the element_identifier from a test parameter it seems - it's a built-in so not surprisingly over-ridden. * rationalise minima for everything. fix dimer minimum of 1 fix tests to conform to new structures * make bed sample small enough * add option for windowed density bigwig output with selectable window size for size selected and specified motifs not so easy for native pytrf operation * fix flake8 issue * more flakery * remove pybigtools to use ucsc-bedgraphtobigwig on a bedgraph instead jbrowse2 simply will not read the bigwigs made using pybigtools :( * Fixes suggested by Bjoern's review * Update tools/microsatbed/microsatbed.xml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Update microsatbed.xml * add help for windowed density bigwig option * fix logic for multiple flags add contents assertions to all tests * remove bogus old merge mark * remove unusual version tokens broken by update bot. --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu> | 25 July 2024, 05:55:37 UTC |
| 025282d | Saim Momin | 24 July 2024, 17:32:50 UTC | Added threads parameter to tool (#6178) | 24 July 2024, 17:32:50 UTC |
| 7b5c842 | Khaled196 | 24 July 2024, 12:46:20 UTC | update tool version (#6175) | 24 July 2024, 12:46:20 UTC |
| 04112de | Pavankumar Videm | 23 July 2024, 16:10:28 UTC | fix pp.make_peak_matrix but and it's test (#6172) | 23 July 2024, 16:10:28 UTC |
| 574cb8c | paulzierep | 23 July 2024, 15:33:44 UTC | Update DeepMicro (#6156) * update params and model export * fix test * version bump, better test, extended help text | 23 July 2024, 15:33:44 UTC |
