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Nicola Soranzo
2515267ca5
instead of relying on `lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml` . Follow-up on https://github.com/galaxyproject/galaxy/pull/5544 . See https://github.com/galaxyproject/galaxy/pull/5544/files#r183909746 for an explanation why that's preferrable for future-proof reproducibility. Also, small fixes to `tools/evolution/codingSnps.xml` .
178 lines
7.9 KiB
XML
178 lines
7.9 KiB
XML
<tool id="hgv_codingSnps" name="aaChanges" version="1.0.1">
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<description>amino-acid changes caused by a set of SNPs</description>
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<requirements>
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<requirement type="package" version="8.25">coreutils</requirement>
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<requirement type="package" version="357">ucsc-twobittofa</requirement>
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<requirement type="package" version="357">ucsc-nibfrag</requirement>
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</requirements>
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<code file="codingSnps_filter.py"></code>
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<command><![CDATA[
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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'
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]]></command>
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<inputs>
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<param format="interval" name="input1" type="data" label="SNP dataset">
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<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" />
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</param>
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<param name="col1" type="data_column" data_ref="input1" label="Column with SNPs" />
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<param format="interval" name="input2" type="data" label="Gene dataset">
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<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" />
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</param>
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<param name="keep" type="select" label="Keep columns from SNP dataset">
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<option value="0" selected="true">No</option>
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<option value="1">Yes</option>
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</param>
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<param name="uniqpos" type="select" label="Only report each SNP position once">
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<option value="1" selected="true">Yes</option>
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<option value="0">No</option>
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</param>
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<conditional name="strand_source">
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<param name="strand_choice" type="select" label="Strand info">
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<option value="data_column">a column in the dataset</option>
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<option value="all_pos" selected="true">all on sense/forward/+ strand</option>
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<option value="all_neg">all on antisense/reverse/- strand</option>
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</param>
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<when value="data_column">
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<param name="strand_col" type="data_column" data_ref="input1" label="Column with strand"/>
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</when>
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<when value="all_pos">
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<param name="strand_col" type="hidden" value="+"/>
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</when>
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<when value="all_neg">
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<param name="strand_col" type="hidden" value="-"/>
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</when>
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</conditional>
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</inputs>
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<outputs>
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<data format="interval" name="out_file1" />
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</outputs>
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<tests>
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<test>
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<param name="input1" ftype="interval" value="codingSnps_input1.interval" dbkey="hg18" />
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<param name="col1" value="6" />
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<param name="input2" ftype="interval" value="codingSnps_inputGenes1.bed" dbkey="hg18" />
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<param name="strand_choice" value="all_pos" />
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<param name="strand_col" value="+" />
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<param name="uniqpos" value="0" />
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<output name="out_file1" file="codingSnps_output1.interval" />
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</test>
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<test>
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<param name="input1" ftype="interval" value="codingSnps_input2.interval" dbkey="hg18" />
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<param name="input2" ftype="interval" value="codingSnps_inputGenes2.bed" dbkey="hg18" />
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<param name="col1" value="4" />
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<param name="strand_choice" value="all_pos" />
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<param name="strand_col" value="+" />
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<param name="uniqpos" value="0" />
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<output name="out_file1" file="codingSnps_output2.interval" />
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</test>
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<test>
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<param name="input1" ftype="interval" value="codingSnps_input2.interval" dbkey="hg18" />
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<param name="input2" ftype="interval" value="codingSnps_inputGenes2.bed" dbkey="hg18" />
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<param name="col1" value="4" />
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<param name="strand_choice" value="all_neg" />
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<param name="strand_col" value="-" />
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<output name="out_file1" file="codingSnps_output3.interval" />
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</test>
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</tests>
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<help>
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.. class:: infomark
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The build must be defined for the input files and must be the same for both files.
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Use the pencil icon to add the build to the files if necessary.
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-----
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**Dataset formats**
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The SNP dataset is in interval_ format, with a column of SNPs as described below.
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The gene dataset is in BED_ format with 12 columns. The output dataset is also interval.
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(`Dataset missing?`_)
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.. _interval: ${static_path}/formatHelp.html#interval
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.. _BED: ${static_path}/formatHelp.html#bed
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.. _Dataset missing?: ${static_path}/formatHelp.html
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-----
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**What it does**
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This tool identifies which SNPs create amino-acid changes in the specified
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coding regions. The first input file contains the SNPs and must be an interval file.
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It needs the chromosome, start, and end position as well as the SNP. The
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SNP can be given using ambiguous-nucleotide symbols or a list of two to four
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alleles
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separated by '/'. Any other columns in the first input file will not be
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used but will be kept for the output. The second input file contains the genes
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to be used for defining the coding regions. This file must be a BED file with
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the first 12 columns standard BED columns. The output is the same as the
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first input file with
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several columns added: the name field from the line of the gene input file
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used, the amino acids, the codon number, the reference nucleotide that
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changed in the amino acid (in the same strand as the gene), and the codons
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that go with the amino acids.
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The amino acids are listed with the reference amino acid first, then a colon,
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and then the amino acids for the alleles. If a SNP is not in a coding region
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or is synonymous then it is not included in the output file.
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-----
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**Example**
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- first input file, with SNPs::
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chr22 15660821 15660822 A/G
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chr22 15825725 15825726 G/T
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chr22 15827035 15827036 G
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chr22 15827135 15827136 C/G
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chr22 15830928 15830929 A/G
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chr22 15830951 15830952 G
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chr22 15830955 15830956 C/T
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chr22 15848885 15848886 C/T
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chr22 15849048 15849049 A/C
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chr22 15919711 15919712 A/G
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etc.
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or, indicating polymorphisms using ambiguous-nucleotide symbols::
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chr22 15660821 15660822 R
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chr22 15825725 15825726 K
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chr22 15827035 15827036 G
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chr22 15827135 15827136 S
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chr22 15830928 15830929 R
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chr22 15830951 15830952 G
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chr22 15830955 15830956 Y
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chr22 15848885 15848886 Y
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chr22 15849048 15849049 M
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chr22 15919711 15919712 R
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etc.
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- second input file, with UCSC annotations for human genes::
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chr22 15688363 15690225 uc010gqr.1 0 + 15688363 15688363 0 2 587,794, 0,1068,
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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,
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chr22 15826991 15869112 uc010gqs.1 0 - 15829218 15869004 0 5 1380,86,157,304,282, 0,2196,21858,25771,41839,
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chr22 15897459 15919682 uc002zlx.1 0 + 15897459 15897459 0 4 775,128,103,1720, 0,8303,10754,20503,
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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,
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etc.
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- output file, showing non-synonymous substitutions in coding regions::
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chr22 15825725 15825726 G/T uc002zlw.1 Gln:Pro/Gln 469 A CAA:CCA/CAA
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chr22 15827035 15827036 G uc002zlw.1 Glu:Asp 414 G GAG:GAC
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chr22 15827135 15827136 C/G uc002zlw.1 Gly:Gly/Ala 381 G GGT:GGT/GCT
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chr22 15830928 15830929 A/G uc002zlw.1 Ala:Ser/Pro 281 G GCA:TCA/CCA
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chr22 15830951 15830952 G uc002zlw.1 Leu:Pro 273 T CTT:CCT
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chr22 15830955 15830956 C/T uc002zlw.1 Ser:Gly/Ser 272 A AGC:GGC/AGC
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chr22 15848885 15848886 C/T uc002zlw.1 Ser:Trp/Stop 217 C TCG:TGG/TAG
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chr22 15848885 15848886 C/T uc010gqs.1 Ser:Trp/Stop 200 C TCG:TGG/TAG
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chr22 15849048 15849049 A/C uc002zlw.1 Gly:Stop/Gly 163 G GGA:TGA/GGA
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etc.
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</help>
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</tool>
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