| cd904d7 | Eric Rasche | 20 March 2017, 18:35:11 UTC | Merge in Dan changes | 20 March 2017, 18:35:11 UTC |
| a149db1 | Eric Rasche | 20 March 2017, 18:21:07 UTC | Merge remote-tracking branch 'dblank/entrez-direct' into entrez-replace | 20 March 2017, 18:21:07 UTC |
| 3363796 | Björn Grüning | 17 March 2017, 18:59:32 UTC | Merge pull request #1197 from cmonjeau/bayescan add bayescan tool | 17 March 2017, 18:59:32 UTC |
| 1af27d5 | Cyril Monjeaud | 17 March 2017, 08:22:28 UTC | Merge branch 'bayescan' of https://github.com/cmonjeau/tools-iuc into bayescan | 17 March 2017, 08:22:28 UTC |
| 6b4c4e1 | Cyril Monjeaud | 17 March 2017, 08:22:05 UTC | add input file in help and remove prefix option | 17 March 2017, 08:22:05 UTC |
| ef28e3f | Anthony Bretaudeau | 14 March 2017, 14:58:43 UTC | Fix travis problem | 14 March 2017, 14:58:43 UTC |
| 37fb198 | yhoogstrate | 14 March 2017, 14:06:30 UTC | Merge pull request #1195 from lparsons/rseqc Migrate RSeQC to IUC | 14 March 2017, 14:06:30 UTC |
| b46aa96 | Marius van den Beek | 13 March 2017, 16:12:12 UTC | Merge pull request #1204 from nsoranzo/data_manager_humann2_database_downloader Fix broken data_manager_humann2_database_downloader | 13 March 2017, 16:12:12 UTC |
| e9e9643 | Nicola Soranzo | 13 March 2017, 15:25:04 UTC | Fix broken data_manager_humann2_database_downloader $ planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error data_managers/data_manager_humann2_database_downloader/ Linting repository /usr/users/ga002/soranzon/software/galaxyproject_tools-iuc/data_managers/data_manager_humann2_database_downloader Error loading tool with path /tmp/planemo_tmp_yfUlf1/83901c99b429ead8a454823bbaa1c331/data_manager_humann2_database_downloader/data_manager/data_manager_humann2_download.xml Traceback (most recent call last): File "/usr/users/ga002/soranzon/software/galaxyproject_planemo/.venv/local/lib/python2.7/site-packages/galaxy/tools/loader_directory.py", line 107, in _load_tools_from_path tool_element = loader_func(possible_tool_file) ParseError: not well-formed (invalid token): line 49, column 32 +Linting tool /usr/users/ga002/soranzon/software/galaxyproject_tools-iuc/data_managers/data_manager_humann2_database_downloader/data_manager/data_manager_humann2_download.xml Could not lint /tmp/planemo_tmp_yfUlf1/83901c99b429ead8a454823bbaa1c331/data_manager_humann2_database_downloader/data_manager/data_manager_humann2_download.xml due to malformed xml. Failed linting Also drop deprecated interpreter attribute of <command>. | 13 March 2017, 15:28:04 UTC |
| 52fa06f | Cyril Monjeaud | 13 March 2017, 14:54:39 UTC | fix travis.yml | 13 March 2017, 14:54:39 UTC |
| 2ed5ffb | Cyril Monjeaud | 13 March 2017, 14:51:39 UTC | Merge branch 'master' into bayescan | 13 March 2017, 14:51:39 UTC |
| e51eb81 | Greg Von Kuster | 13 March 2017, 12:41:58 UTC | Merge pull request #1196 from gregvonkuster/multigps Add MultiGPS version 0.73.0 | 13 March 2017, 12:41:58 UTC |
| 3e179ac | Björn Grüning | 12 March 2017, 18:09:31 UTC | Merge pull request #1192 from galaxyproject/humann2 Add a wrapper for HUMAnN2 | 12 March 2017, 18:09:31 UTC |
| 1074783 | Marius van den Beek | 12 March 2017, 08:04:49 UTC | Merge pull request #1201 from bwlang/patch-3 samtools 1.2 needs more params to reliably sort | 12 March 2017, 08:04:49 UTC |
| bf6322c | Brad Langhorst | 12 March 2017, 03:07:04 UTC | samtools 1.2 needs more params to reliably sort without these options it gets into legacy mode and the tool break see: https://github.com/samtools/samtools/issues/349 | 12 March 2017, 03:07:04 UTC |
| 3edcac6 | Björn Grüning | 11 March 2017, 22:15:53 UTC | Merge pull request #1199 from nsoranzo/bcftools Condafy bcftools | 11 March 2017, 22:15:53 UTC |
| 7bb9041 | Nicola Soranzo | 09 March 2017, 21:11:11 UTC | Remove tool_dependencies.xml . Update requirements. Lint 2 files | 10 March 2017, 17:33:45 UTC |
| 5f26485 | Björn Grüning | 10 March 2017, 13:52:24 UTC | Add travis_wait to prevent the 10min no output error. | 10 March 2017, 13:52:24 UTC |
| 8bb1d44 | Cyril Monjeaud | 10 March 2017, 10:11:28 UTC | add .shed.yml | 10 March 2017, 10:11:28 UTC |
| 3f99650 | Cyril Monjeaud | 10 March 2017, 10:11:13 UTC | improve indentation and boolean parameters and remove citations | 10 March 2017, 10:11:13 UTC |
| 4b6669d | Björn Grüning | 10 March 2017, 09:33:15 UTC | Pipe the output of planemo conda_install to /dev/null for the time being | 10 March 2017, 09:33:15 UTC |
| 010c0a8 | Greg Von Kuster | 09 March 2017, 13:58:47 UTC | Add README and details for memory allocation to help text | 09 March 2017, 13:58:47 UTC |
| ed37159 | Greg Von Kuster | 09 March 2017, 13:02:21 UTC | Tweaks per initial review | 09 March 2017, 13:02:21 UTC |
| 2431a12 | Cyril Monjeaud | 09 March 2017, 10:53:26 UTC | add bayescan tool | 09 March 2017, 10:53:26 UTC |
| fa84b74 | Lance Parsons | 09 March 2017, 02:14:45 UTC | Cleanup of read_hexamer.xml | 09 March 2017, 02:14:45 UTC |
| dfe5b3e | Lance Parsons | 08 March 2017, 22:53:06 UTC | Moved rseqc images to local repo | 08 March 2017, 22:53:06 UTC |
| 5dcaef1 | Lance Parsons | 08 March 2017, 22:30:01 UTC | Converted conditionals from boolean to select | 08 March 2017, 22:30:01 UTC |
| ebc7ae8 | Lance Parsons | 08 March 2017, 19:09:51 UTC | Fix a couple of rseqc tests geneBody_coverage2 and read_quality test outputs were misnamed | 08 March 2017, 20:05:29 UTC |
| f8b0cc1 | Lance Parsons | 08 March 2017, 19:03:08 UTC | Added transcriptomics to rseqc categories | 08 March 2017, 19:03:08 UTC |
| 38a06e2 | Lance Parsons | 08 March 2017, 18:56:55 UTC | Ensure multiple inputs get unique identifiers | 08 March 2017, 18:56:55 UTC |
| 220e5a8 | Lance Parsons | 07 March 2017, 16:53:24 UTC | Moved more params to macros | 07 March 2017, 16:53:24 UTC |
| 8fc4caf | Lance Parsons | 07 March 2017, 16:31:00 UTC | Standardized linking command to | 07 March 2017, 16:31:00 UTC |
| 9c6a092 | Lance Parsons | 07 March 2017, 16:00:21 UTC | Fixed syntax for select params Used selected="true" for defaults instead of setting value. Also added min to sample_size param for infer_experiment. | 07 March 2017, 16:00:21 UTC |
| 2baef63 | Lance Parsons | 06 March 2017, 19:07:48 UTC | Make R script outputs optional Make R Script outputs optional for tools that output this type. Use macros to improve consistency across tools. | 06 March 2017, 19:07:48 UTC |
| a5bdf15 | Greg Von Kuster | 06 March 2017, 16:19:16 UTC | Add MultiGPS version 0.73.0 | 06 March 2017, 16:19:16 UTC |
| 189ba75 | Lance Parsons | 06 March 2017, 16:18:14 UTC | Remove obsolete toolshed packages | 06 March 2017, 16:18:14 UTC |
| 777ea6a | Bérénice Batut | 06 March 2017, 09:57:51 UTC | Remove useless stdio | 06 March 2017, 09:57:51 UTC |
| 0a52272 | Bérénice Batut | 06 March 2017, 08:33:11 UTC | Correct version command | 06 March 2017, 08:33:11 UTC |
| c071271 | Bérénice Batut | 06 March 2017, 07:47:38 UTC | Add sections and clean humann2.xml | 06 March 2017, 08:21:19 UTC |
| 8b19e42 | Bérénice Batut | 05 March 2017, 18:06:22 UTC | Fix file copy for join table | 05 March 2017, 18:06:22 UTC |
| 851dcb5 | Bérénice Batut | 05 March 2017, 17:51:44 UTC | Fix help header | 05 March 2017, 17:51:44 UTC |
| 0bcea92 | Bérénice Batut | 05 March 2017, 17:44:39 UTC | Change simple quotes to double quotes in inputs and tests | 05 March 2017, 17:44:39 UTC |
| 90047c2 | Bérénice Batut | 05 March 2017, 17:33:50 UTC | Correct default in README | 05 March 2017, 17:33:50 UTC |
| 0fd3b94 | Bérénice Batut | 05 March 2017, 17:31:38 UTC | Merge branch 'humann2' of https://github.com/galaxyproject/tools-iuc into humann2 | 05 March 2017, 17:31:38 UTC |
| 2bbe1ca | Bérénice Batut | 05 March 2017, 17:29:36 UTC | Remove the repeat in favor of multiple | 05 March 2017, 17:29:36 UTC |
| e923567 | Bérénice Batut | 05 March 2017, 17:28:46 UTC | Remove useless test files | 05 March 2017, 17:28:46 UTC |
| 01fc0ca | Bérénice Batut | 05 March 2017, 17:09:29 UTC | Correct biom format | 05 March 2017, 17:09:29 UTC |
| eb4183e | Bérénice Batut | 05 March 2017, 17:07:17 UTC | Change simple quotes to double quotes in inputs and tests | 05 March 2017, 17:07:17 UTC |
| 3bd2611 | Bérénice Batut | 05 March 2017, 17:01:03 UTC | Remove help redundancy | 05 March 2017, 17:01:03 UTC |
| 57cff37 | Bérénice Batut | 05 March 2017, 16:59:58 UTC | Add tabular to tsv for inputs | 05 March 2017, 16:59:58 UTC |
| 332f289 | Bérénice Batut | 05 March 2017, 16:54:23 UTC | Correct link to tool website | 05 March 2017, 16:54:23 UTC |
| c226149 | Bérénice Batut | 05 March 2017, 16:53:15 UTC | Remove remaining false help | 05 March 2017, 16:53:15 UTC |
| 2868edf | Bérénice Batut | 05 March 2017, 16:50:27 UTC | Move help header to macros | 05 March 2017, 16:50:27 UTC |
| 08cd8e9 | Bérénice Batut | 05 March 2017, 16:43:58 UTC | Change version and replace error detection | 05 March 2017, 16:43:58 UTC |
| 10372ff | Björn Grüning | 04 March 2017, 17:50:46 UTC | This is needed maybe needed for the tool to not exceed to much memory. | 04 March 2017, 17:50:46 UTC |
| c1353d3 | Bérénice Batut | 04 March 2017, 17:04:47 UTC | Try to force diamond to use less threads | 04 March 2017, 17:04:47 UTC |
| 345fb7e | Björn Grüning | 04 March 2017, 16:51:02 UTC | Merge pull request #1182 from galaxyproject/metaphlan2 Add wrapper for MetaPhlAn2 and a data manager for its database | 04 March 2017, 16:51:02 UTC |
| 2411a61 | Björn Grüning | 04 March 2017, 16:39:04 UTC | Merge pull request #1193 from galaxyproject/export2graphlan Add wrapper for export2graphlan | 04 March 2017, 16:39:04 UTC |
| d9cedb1 | Björn Grüning | 04 March 2017, 16:28:33 UTC | Update export2graphlan.xml | 04 March 2017, 16:28:33 UTC |
| 6e73e77 | Björn Grüning | 04 March 2017, 15:17:40 UTC | Merge pull request #1194 from galaxyproject/graphlan Add wrapper for GraPhlAn | 04 March 2017, 15:17:40 UTC |
| bae4266 | Bérénice Batut | 04 March 2017, 15:09:54 UTC | Add dpi in condition | 04 March 2017, 15:09:54 UTC |
| 21ae197 | Lance Parsons | 03 March 2017, 18:59:12 UTC | Upgrade to RSeQC 2.6.4 Move to IUC, added some new tools, updated tests, use element_identifier where appropriate. | 04 March 2017, 14:39:49 UTC |
| 02a48f0 | Bérénice Batut | 04 March 2017, 13:14:31 UTC | Add citation | 04 March 2017, 13:14:31 UTC |
| c3b2bf5 | Björn Grüning | 03 March 2017, 20:47:20 UTC | Merge pull request #1188 from lparsons/nugen_nudup_2_3_2 Update Nugen NuDUP to 2.3.2 | 03 March 2017, 20:47:20 UTC |
| 626b990 | Björn Grüning | 03 March 2017, 18:22:44 UTC | Merge pull request #1191 from nsoranzo/abricate_prinseq Condafy abricate and prinseq | 03 March 2017, 18:22:44 UTC |
| 62a8830 | Bérénice Batut | 03 March 2017, 15:18:50 UTC | Add wrapper for GraPhlAn | 03 March 2017, 15:29:39 UTC |
| d2308c8 | Bérénice Batut | 03 March 2017, 14:45:03 UTC | Add wrapper for export2graphlan | 03 March 2017, 14:45:03 UTC |
| 4037b10 | Bérénice Batut | 03 March 2017, 14:00:10 UTC | Add files for testing metaphlan2 use | 03 March 2017, 14:00:10 UTC |
| 66924cf | Bérénice Batut | 03 March 2017, 13:23:33 UTC | Replace double by simple quotes | 03 March 2017, 13:23:33 UTC |
| 22b74fc | Bérénice Batut | 03 March 2017, 13:19:14 UTC | Replace double quotes | 03 March 2017, 13:19:14 UTC |
| bc6905d | Bérénice Batut | 03 March 2017, 13:18:52 UTC | Modify a bit the doc about the inputs | 03 March 2017, 13:18:52 UTC |
| f8982ff | Bérénice Batut | 03 March 2017, 12:59:00 UTC | Fix use of history db for metaphlan2 | 03 March 2017, 12:59:00 UTC |
| e1615d1 | Bérénice Batut | 03 March 2017, 12:41:43 UTC | Correct metaphlan2 options | 03 March 2017, 12:41:43 UTC |
| cdcc4b8 | Bérénice Batut | 03 March 2017, 12:17:34 UTC | Add missing test data for humann2 | 03 March 2017, 12:17:34 UTC |
| c223aa5 | Bérénice Batut | 03 March 2017, 12:14:54 UTC | Change the README content | 03 March 2017, 12:14:54 UTC |
| 38c128d | Bérénice Batut | 03 March 2017, 09:54:11 UTC | Correct flake8 | 03 March 2017, 11:02:01 UTC |
| 6e6c921 | Bérénice Batut | 03 March 2017, 09:48:44 UTC | Change the data manager value and the path to database | 03 March 2017, 09:48:44 UTC |
| 5380ed0 | Nicola Soranzo | 02 March 2017, 19:36:42 UTC | Condafy abricate and prinseq Remove tool_dependencies.xml Remove requirements included in main package. Single-quote dataset paths in <command> Cast optional integer/float params to string when checking if they are set. Update abricate test data. | 02 March 2017, 19:50:39 UTC |
| cf8373a | Bérénice Batut | 02 March 2017, 16:11:34 UTC | Extract tax level to macros | 02 March 2017, 16:19:41 UTC |
| eb3d284 | Daniel Blankenberg | 02 March 2017, 16:18:00 UTC | Update to version 5.80 | 02 March 2017, 16:18:00 UTC |
| f45f315 | Bérénice Batut | 02 March 2017, 16:04:59 UTC | Change the defualt seleted option for translated alignment | 02 March 2017, 16:04:59 UTC |
| 5b80101 | Bérénice Batut | 02 March 2017, 16:04:17 UTC | Correct the extraction of the path to metaphlan2 db | 02 March 2017, 16:04:17 UTC |
| e92ff87 | Daniel Blankenberg | 02 March 2017, 16:02:45 UTC | Merge branch 'master' of https://github.com/galaxyproject/tools-iuc into entrez-direct | 02 March 2017, 16:02:45 UTC |
| adf6952 | Bérénice Batut | 02 March 2017, 14:11:21 UTC | Correct the tool data table conf for metaphlan2 table | 02 March 2017, 14:11:21 UTC |
| 13074f3 | Bérénice Batut | 02 March 2017, 14:10:35 UTC | Correct db parameters | 02 March 2017, 14:10:35 UTC |
| cafbccd | Bérénice Batut | 02 March 2017, 14:09:02 UTC | Remove extra spaces | 02 March 2017, 14:09:02 UTC |
| 3145b00 | Bérénice Batut | 02 March 2017, 14:07:51 UTC | Rename and move the downloaded db | 02 March 2017, 14:07:51 UTC |
| 68b2b95 | Bérénice Batut | 02 March 2017, 14:06:59 UTC | Correct the data manager configuration | 02 March 2017, 14:06:59 UTC |
| 318eb33 | Bérénice Batut | 01 March 2017, 16:53:37 UTC | Correct path | 01 March 2017, 16:53:37 UTC |
| 0b32b29 | Bérénice Batut | 01 March 2017, 16:47:49 UTC | Add humann2 wrappers | 01 March 2017, 16:47:49 UTC |
| 0354c72 | Bérénice Batut | 01 March 2017, 16:46:41 UTC | Add a data manager for humann2 | 01 March 2017, 16:47:12 UTC |
| 38ee3fb | Bérénice Batut | 01 March 2017, 16:15:14 UTC | Fix flake8 | 01 March 2017, 16:15:14 UTC |
| 0076dad | Bérénice Batut | 01 March 2017, 15:11:20 UTC | Remove sample naming arguments | 01 March 2017, 15:11:20 UTC |
| 09369e9 | Bérénice Batut | 01 March 2017, 15:09:41 UTC | Remove bowtie test | 01 March 2017, 15:09:41 UTC |
| b30ab72 | Bérénice Batut | 01 March 2017, 15:09:11 UTC | Use last bowtie version and add python version | 01 March 2017, 15:09:11 UTC |
| 0a6ab4f | Bérénice Batut | 01 March 2017, 15:07:16 UTC | Rename metaphlan_hclust_heatmap.xml | 01 March 2017, 15:07:16 UTC |
| 20127f5 | Bérénice Batut | 01 March 2017, 15:06:55 UTC | Rename merge_metaphlan_tables | 01 March 2017, 15:06:55 UTC |
| 74b7b30 | Bérénice Batut | 01 March 2017, 15:06:36 UTC | Fix the owner of the required repository | 01 March 2017, 15:06:36 UTC |
| 0975aac | Bérénice Batut | 01 March 2017, 15:05:25 UTC | Move the downloaded db | 01 March 2017, 15:05:25 UTC |
| 594a662 | Bérénice Batut | 01 March 2017, 15:04:55 UTC | Change the possible db_key | 01 March 2017, 15:04:55 UTC |
