comparison maxquant_mqpar.xml @ 4:d0485bab76b8 draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"

3:f9c1f29d9711

    --num_threads=\${GALAXY_SLOTS:-1}
    --substitution_rx='@SUBSTITUTION_RX@'
    --fasta_files='$fasta_files'
    --description_parse_rule='$description_parse_rule'
    --identifier_parse_rule='$identifier_parse_rule'
    '$mqpar'

    &&
    maxquant mqpar.xml
    #if 'log' in $output:
        >> '$log'
    #end if
    && mv '$mqpar' combined/txt/mqpar.xml
    #if 'output_all' in $output:
        &&
        tar -zcf '$output_all' ./combined/txt
    #end if
  

                <valid initial="string.printable">
                    <remove value="&apos;"/>
                </valid>
            </sanitizer>
        </param>
        <param type="data" name="mqpar" format="xml"
               label="mqpar.xml file with your search parameters. RAW file names 
                      must match the names displayed in galaxy. Their paths 
                      from the local machine are ignored. E.g. a file named
                      'test01.raw' in galaxy can either be named 'test01.raw' or
                      'D:\path\to\test01.raw' in the mqpar.xml."/>

            <param name="ftype" value=".mzxml" />
            <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" value="mqpar.xml" />
            <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,output_all" />
            <output name="evidence" file="txt/evidence.txt" />
            <output name="msms" file="txt/msms.txt" lines_diff="2" />
            <output name="allPeptides" file="txt/allPeptides.txt" lines_diff="32" />
            <output name="msmsScans" file="txt/msmsScans.txt" lines_diff="4"/>
            <output name="mzRange" file="txt/mzRange.txt" />
            <output name="parameters" file="txt/parameters.txt" lines_diff="8"/>
            <output name="peptides" file="txt/peptides.txt" />
            <output name="proteinGroups" file="txt/proteinGroups.txt" />
            <output name="summary" file="txt/summary.txt" />
            <output name="modificationSpecificPeptides" file="txt/modificationSpecificPeptides.txt" />
        </test>
    </tests>
    <help><![CDATA[
MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. 

4:d0485bab76b8

    --num_threads=\${GALAXY_SLOTS:-1}
    --substitution_rx='@SUBSTITUTION_RX@'
    --fasta_files='$fasta_files'
    --description_parse_rule='$description_parse_rule'
    --identifier_parse_rule='$identifier_parse_rule'
    '$mqpar_input'

    &&
    maxquant mqpar.xml
    #if 'log' in $output:
        >> '$log'
    #end if
    && mv mqpar.xml combined/txt/mqpar.xml
    #if 'output_all' in $output:
        &&
        tar -zcf '$output_all' ./combined/txt
    #end if
  

                <valid initial="string.printable">
                    <remove value="&apos;"/>
                </valid>
            </sanitizer>
        </param>
        <param type="data" name="mqpar_input" format="xml"
               label="mqpar.xml file with your search parameters. RAW file names 
                      must match the names displayed in galaxy. Their paths 
                      from the local machine are ignored. E.g. a file named
                      'test01.raw' in galaxy can either be named 'test01.raw' or
                      'D:\path\to\test01.raw' in the mqpar.xml."/>

            <param name="ftype" value=".mzxml" />
            <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.xml" />
            <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,mqpar,output_all" />
            <output name="evidence" file="txt/evidence.txt" />
            <output name="msms" file="txt/msms.txt" lines_diff="2" />
            <output name="allPeptides" file="txt/allPeptides.txt" lines_diff="32" />
            <output name="msmsScans" file="txt/msmsScans.txt" lines_diff="4"/>
            <output name="mzRange" file="txt/mzRange.txt" />
            <output name="parameters" file="txt/parameters.txt" lines_diff="8"/>
            <output name="peptides" file="txt/peptides.txt" />
            <output name="proteinGroups" file="txt/proteinGroups.txt" />
            <output name="summary" file="txt/summary.txt" />
            <output name="modificationSpecificPeptides" file="txt/modificationSpecificPeptides.txt" />
            <output name="mqpar" file="txt/mqpar.xml" lines_diff="8" />
        </test>
    </tests>
    <help><![CDATA[
MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.