comparison maxquant_mqpar.xml @ 21:8934bc76bb52 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb

20:837224ad1694

<tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@+galaxy@VERSION_SUFFIX_MQPAR@" profile="21.05">
    <macros>
        <xml name="output" token_format="tabular" token_label="default description" token_name="default">
            <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">
                <filter>'@NAME@' in output</filter>
            </data>
        </xml>
        <xml name="output_from_wdir" token_ext="txt" token_format="tabular" token_label="default description" token_name="default">
            <data format="@FORMAT@" from_work_dir="combined/txt/@NAME@.@EXT@" label="@LABEL@ for ${on_string}" name="@NAME@">
                <filter>'@NAME@' in output</filter>
            </data>
        </xml>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="required_files"/>
    <command detect_errors="exit_code"><![CDATA[

    #if 'output_all' in $output:
        &&
        tar -zcf '$output_all' ./combined/txt
    #end if
  
    #if $qc.do_it:
        &&
        Rscript '$qr' '$qr_yaml'
        #if 'log' in $output:
            >> '$log' 2>&1
        #end if

            <param name="infiles" value="BSA_min_22,BSA_min_21.mzXML" />
            <param name="fasta_files" value="bsa.fasta" />
            <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
            <param name="description_parse_rule" value="&gt;(.*)" />
            <param name="mqpar_input" value="mqpar/mqpar.xml" />
            <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,mqpar,output_all" />
            <output name="evidence">
                <assert_contents>
                    <has_text text="AEFVEVTK" />
                </assert_contents>
            </output>

21:8934bc76bb52

<tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@+galaxy@VERSION_SUFFIX_MQPAR@" profile="@PROFILE@">
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="required_files"/>
    <command detect_errors="exit_code"><![CDATA[

    #if 'output_all' in $output:
        &&
        tar -zcf '$output_all' ./combined/txt
    #end if
  
    #if $qc.do_it == 'true':
        &&
        Rscript '$qr' '$qr_yaml'
        #if 'log' in $output:
            >> '$log' 2>&1
        #end if

            <param name="infiles" value="BSA_min_22,BSA_min_21.mzXML" />
            <param name="fasta_files" value="bsa.fasta" />
            <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
            <param name="description_parse_rule" value="&gt;(.*)" />
            <param name="mqpar_input" value="mqpar/mqpar.xml" />
            <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,proteinGroups,summary,modificationSpecificPeptides,mqpar,output_all" />
            <output name="evidence">
                <assert_contents>
                    <has_text text="AEFVEVTK" />
                </assert_contents>
            </output>