comparison map_peptides_to_bed.xml @ 2:78b8213e122d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed commit bd3b68ee27bc3b50b9970d4fe801cb1a13900f4c

1:db90662d26f9

<tool id="map_peptides_to_bed" name="Map peptides to a bed file" version="0.1.0">
    <description>for viewing in a genome browser</description>
    <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" 
               help="mapping Protein IDs from a Protein Search fasta to a reference genome"/>
        <param name="input" type="data" format="tabular" label="Identified Peptides" 

    <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>

2:78b8213e122d

<tool id="map_peptides_to_bed" name="Map peptides to a bed file" version="0.1.1">
    <description>for viewing in a genome browser</description>
    <requirements>
        <requirement type="package" version="1.62">biopython</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        python '$__tool_directory__/map_peptides_to_bed.py'
          --translated_bed='$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" 
               help="mapping Protein IDs from a Protein Search fasta to a reference genome"/>
        <param name="input" type="data" format="tabular" label="Identified Peptides" 

    <outputs>
        <data name="mapped_peptides" format="bed" />
    </outputs>
    <tests>
        <test>
            <param name="translated_bed" ftype="bed" value="translated_bed_sequences.bed"/>
            <param name="input" 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>