Mercurial > repos > galaxyp > map_peptides_to_bed
view map_peptides_to_bed.xml @ 0:51f8f9041724 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
author | galaxyp |
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date | Mon, 25 Jan 2016 15:32:49 -0500 |
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children | db90662d26f9 |
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<tool id="map_peptides_to_bed" name="Map peptides to a bed file" version="0.1.0"> <requirements> <requirement type="package" version="1.62">biopython</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command interpreter="python"><![CDATA[ map_peptides_to_bed.py --translated_bed="$translated_bed" --input="$input" #if $peptide_column: --peptide_column=$peptide_column #end if #if $name_column: --name_column=$name_column #end if #if $start_column: --start_column=$start_column #end if $gffTags --bed="$mapped_peptides" ]]></command> <inputs> <param name="translated_bed" type="data" format="bed" label="Translated bed with IDs to match in the input" help=""/> <param name="input" type="data" format="tabular" label="Identified Peptides" help=""/> <param name="peptide_column" type="data_column" data_ref="input" label="peptide column" optional="true" help="Defaults to first column"/> <param name="name_column" type="data_column" data_ref="input" label="protein name column" optional="true" help="The name in this column must match the name column in the Translate bed"/> <param name="start_column" type="data_column" data_ref="input" label="peptide offset column" optional="true" help="The offset in AnimoAcids of the peptide from the start of the protein sequence"/> <param name="gffTags" type="boolean" truevalue="--gffTags" falsevalue="" checked="true" label="Use #gffTags in output" help=""/> </inputs> <outputs> <data name="mapped_peptides" format="bed" /> </outputs> <tests> <test> <param name="translated_bed" type="data" ftype="bed" value="translated_bed_sequences.bed"/> <param name="input" type="data" ftype="tabular" value="peptides.tsv"/> <param name="peptide_column" value="2"/> <param name="name_column" value="1"/> <output name="mapped_peptides" file="mapped_peptides.bed"/> </test> </tests> <help><![CDATA[ Usage: map_peptides_to_bed.py [options] Options: -h, --help show this help message and exit -t TRANSLATED_BED, --translated_bed=TRANSLATED_BED A bed file with added 13th column having a translation -i INPUT, --input=INPUT Tabular file with peptide_sequence column -p PEPTIDE_COLUMN, --peptide_column=PEPTIDE_COLUMN column ordinal with peptide sequence -n NAME_COLUMN, --name_column=NAME_COLUMN column ordinal with protein name -s START_COLUMN, --start_column=START_COLUMN column with peptide start position in protein -B BED, --bed=BED Output a bed file with added 13th column having translation -T, --gffTags Add #gffTags to bed output for IGV -d, --debug Turn on wrapper debugging to stderr ]]></help> </tool>