https://github.com/galaxyproject/galaxy
Tip revision: 95036639dd4f7bd986e93acc99d5dd1be7823286 authored by Dannon Baker on 11 April 2023, 13:10:41 UTC
Update version to 23.0.
Update version to 23.0.
Tip revision: 9503663
codingSnps.xml
<tool id="hgv_codingSnps" name="aaChanges" version="1.0.1">
<description>amino-acid changes caused by a set of SNPs</description>
<requirements>
<requirement type="package" version="8.25">coreutils</requirement>
<requirement type="package" version="357">ucsc-twobittofa</requirement>
<requirement type="package" version="357">ucsc-nibfrag</requirement>
</requirements>
<code file="codingSnps_filter.py"></code>
<command><![CDATA[
perl '$__tool_directory__/codingSnps.pl' '$input1' '$input2' Galaxy build=${input1.metadata.dbkey} loc=${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 keepColumns=$keep strand=${strand_source.strand_col} unique=$uniqpos > '$out_file1'
]]></command>
<inputs>
<param format="interval" name="input1" type="data" label="SNP dataset">
<validator type="dataset_metadata_in_file" filename="codingSnps.loc" metadata_name="dbkey" metadata_column="0" message="Sequences are not currently available for the specified build." split="\t" />
</param>
<param name="col1" type="data_column" data_ref="input1" label="Column with SNPs" />
<param format="interval" name="input2" type="data" label="Gene dataset">
<validator type="dataset_metadata_in_file" filename="codingSnps.loc" metadata_name="dbkey" metadata_column="0" message="Sequences are not currently available for the specified build." split="\t" />
</param>
<param name="keep" type="select" label="Keep columns from SNP dataset">
<option value="0" selected="true">No</option>
<option value="1">Yes</option>
</param>
<param name="uniqpos" type="select" label="Only report each SNP position once">
<option value="1" selected="true">Yes</option>
<option value="0">No</option>
</param>
<conditional name="strand_source">
<param name="strand_choice" type="select" label="Strand info">
<option value="data_column">a column in the dataset</option>
<option value="all_pos" selected="true">all on sense/forward/+ strand</option>
<option value="all_neg">all on antisense/reverse/- strand</option>
</param>
<when value="data_column">
<param name="strand_col" type="data_column" data_ref="input1" label="Column with strand"/>
</when>
<when value="all_pos">
<param name="strand_col" type="hidden" value="+"/>
</when>
<when value="all_neg">
<param name="strand_col" type="hidden" value="-"/>
</when>
</conditional>
</inputs>
<outputs>
<data format="interval" name="out_file1" />
</outputs>
<tests>
<test>
<param name="input1" ftype="interval" value="codingSnps_input1.interval" dbkey="hg18" />
<param name="col1" value="6" />
<param name="input2" ftype="interval" value="codingSnps_inputGenes1.bed" dbkey="hg18" />
<param name="strand_choice" value="all_pos" />
<param name="strand_col" value="+" />
<param name="uniqpos" value="0" />
<output name="out_file1" file="codingSnps_output1.interval" />
</test>
<test>
<param name="input1" ftype="interval" value="codingSnps_input2.interval" dbkey="hg18" />
<param name="input2" ftype="interval" value="codingSnps_inputGenes2.bed" dbkey="hg18" />
<param name="col1" value="4" />
<param name="strand_choice" value="all_pos" />
<param name="strand_col" value="+" />
<param name="uniqpos" value="0" />
<output name="out_file1" file="codingSnps_output2.interval" />
</test>
<test>
<param name="input1" ftype="interval" value="codingSnps_input2.interval" dbkey="hg18" />
<param name="input2" ftype="interval" value="codingSnps_inputGenes2.bed" dbkey="hg18" />
<param name="col1" value="4" />
<param name="strand_choice" value="all_neg" />
<param name="strand_col" value="-" />
<output name="out_file1" file="codingSnps_output3.interval" />
</test>
</tests>
<help>
.. class:: infomark
The build must be defined for the input files and must be the same for both files.
Use the pencil icon to add the build to the files if necessary.
-----
**Dataset formats**
The SNP dataset is in interval_ format, with a column of SNPs as described below.
The gene dataset is in BED_ format with 12 columns. The output dataset is also interval.
(`Dataset missing?`_)
.. _interval: ${static_path}/formatHelp.html#interval
.. _BED: ${static_path}/formatHelp.html#bed
.. _Dataset missing?: ${static_path}/formatHelp.html
-----
**What it does**
This tool identifies which SNPs create amino-acid changes in the specified
coding regions. The first input file contains the SNPs and must be an interval file.
It needs the chromosome, start, and end position as well as the SNP. The
SNP can be given using ambiguous-nucleotide symbols or a list of two to four
alleles
separated by '/'. Any other columns in the first input file will not be
used but will be kept for the output. The second input file contains the genes
to be used for defining the coding regions. This file must be a BED file with
the first 12 columns standard BED columns. The output is the same as the
first input file with
several columns added: the name field from the line of the gene input file
used, the amino acids, the codon number, the reference nucleotide that
changed in the amino acid (in the same strand as the gene), and the codons
that go with the amino acids.
The amino acids are listed with the reference amino acid first, then a colon,
and then the amino acids for the alleles. If a SNP is not in a coding region
or is synonymous then it is not included in the output file.
-----
**Example**
- first input file, with SNPs::
chr22 15660821 15660822 A/G
chr22 15825725 15825726 G/T
chr22 15827035 15827036 G
chr22 15827135 15827136 C/G
chr22 15830928 15830929 A/G
chr22 15830951 15830952 G
chr22 15830955 15830956 C/T
chr22 15848885 15848886 C/T
chr22 15849048 15849049 A/C
chr22 15919711 15919712 A/G
etc.
or, indicating polymorphisms using ambiguous-nucleotide symbols::
chr22 15660821 15660822 R
chr22 15825725 15825726 K
chr22 15827035 15827036 G
chr22 15827135 15827136 S
chr22 15830928 15830929 R
chr22 15830951 15830952 G
chr22 15830955 15830956 Y
chr22 15848885 15848886 Y
chr22 15849048 15849049 M
chr22 15919711 15919712 R
etc.
- second input file, with UCSC annotations for human genes::
chr22 15688363 15690225 uc010gqr.1 0 + 15688363 15688363 0 2 587,794, 0,1068,
chr22 15822826 15869112 uc002zlw.1 0 - 15823622 15869004 0 10 940,105,97,91,265,86,251,208,304,282, 0,1788,2829,3241,4163,6361,8006,26023,29936,46004,
chr22 15826991 15869112 uc010gqs.1 0 - 15829218 15869004 0 5 1380,86,157,304,282, 0,2196,21858,25771,41839,
chr22 15897459 15919682 uc002zlx.1 0 + 15897459 15897459 0 4 775,128,103,1720, 0,8303,10754,20503,
chr22 15945848 15971389 uc002zly.1 0 + 15945981 15970710 0 13 271,25,147,113,127,48,164,84,85,12,102,42,2193, 0,12103,12838,13816,15396,17037,17180,18535,19767,20632,20894,22768,23348,
etc.
- output file, showing non-synonymous substitutions in coding regions::
chr22 15825725 15825726 G/T uc002zlw.1 Gln:Pro/Gln 469 A CAA:CCA/CAA
chr22 15827035 15827036 G uc002zlw.1 Glu:Asp 414 G GAG:GAC
chr22 15827135 15827136 C/G uc002zlw.1 Gly:Gly/Ala 381 G GGT:GGT/GCT
chr22 15830928 15830929 A/G uc002zlw.1 Ala:Ser/Pro 281 G GCA:TCA/CCA
chr22 15830951 15830952 G uc002zlw.1 Leu:Pro 273 T CTT:CCT
chr22 15830955 15830956 C/T uc002zlw.1 Ser:Gly/Ser 272 A AGC:GGC/AGC
chr22 15848885 15848886 C/T uc002zlw.1 Ser:Trp/Stop 217 C TCG:TGG/TAG
chr22 15848885 15848886 C/T uc010gqs.1 Ser:Trp/Stop 200 C TCG:TGG/TAG
chr22 15849048 15849049 A/C uc002zlw.1 Gly:Stop/Gly 163 G GGA:TGA/GGA
etc.
</help>
</tool>