comparison msgfplus.xml @ 9:a26f5807eb85 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 75603eb19ef066d891fd906d7dd4b06f5498ca68

8:09e0ae6f661b

<tool id="msgfplus" name="MS-GF+" version="0.4">
    <description>
        Identifies peptides in tandem mass spectra using the MS-GF+ search engine.
    </description>
    <requirements>
        <requirement type="package" version="2017.07.21">msgf_plus</requirement>

            -maxLength $advanced.maxLength
            -minCharge $advanced.minCharge
            -maxCharge $advanced.maxCharge
            -n $advanced.n
            -addFeatures $advanced.addFeatures
        #if $tsvcheck
            &&
            msgf_plus
              edu.ucsd.msjava.ui.MzIDToTsv
              -i '$output_name'
              -o output.tsv
        #end if
        &&
        mv '$output_name' output
]]>
    </command>

              <when value="fractions">
                  <param name="db_spectra" type="data_collection" collection_type="paired" 
                      label="Collection: Pairs of spectra (forward) and FASTA database (reverse)"/>
              </when>
        </conditional>
        <param name="tsvcheck" type="boolean" label="Output TSV as well?" />
        <param argument="-tda" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Search with on-the-fly decoy database?" help="MSGF+ uses XXX_ as an accession prefix to indicate a decoy hit" />
        <param argument="-t" type="float" value="10" label="Precursor mass tolerance" help="Error tolerance for matching peptide mass to precursor ion mass"/>
        <param name="precursor_ion_tol_units" type="select" label="Precursor mass tolerance units" help="Daltons are common for low-res instruments, ppm for high-res instruments">
            <option value="ppm" selected="true">Parts per million (ppm)</option>
            <option value="Da">Daltons</option>

        </test>
        <test>
            <param name="msgf_input|intype_selector" value="single" />
            <param name="msgf_input|s" value="input/201208-378803.mzML" />
            <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" />
            <param name="tsvcheck" value="true" />
            <param name="tda" value="1" />
            <param name="ntt" value="1" />
            <param name="t" value="50" />
            <param name="precursor_ion_tol_units" value="ppm" />
            <param name="common_fixed_modifications" value="" />

9:a26f5807eb85

<tool id="msgfplus" name="MS-GF+" version="0.5">
    <description>
        Identifies peptides in tandem mass spectra using the MS-GF+ search engine.
    </description>
    <requirements>
        <requirement type="package" version="2017.07.21">msgf_plus</requirement>

            -maxLength $advanced.maxLength
            -minCharge $advanced.minCharge
            -maxCharge $advanced.maxCharge
            -n $advanced.n
            -addFeatures $advanced.addFeatures
        #if $tsv == 'targets' or $tsv == 'decoys' 
	    &&
	    msgf_plus
	        edu.ucsd.msjava.ui.MzIDToTsv
	        -i '$output_name'
	        -o output.tsv
            #if $tsv == 'decoys'
                -showDecoy 1
            #end if
        #end if
        &&
        mv '$output_name' output
]]>
    </command>

              <when value="fractions">
                  <param name="db_spectra" type="data_collection" collection_type="paired" 
                      label="Collection: Pairs of spectra (forward) and FASTA database (reverse)"/>
              </when>
        </conditional>
        <param name="tsv" type="select" label="Output TSV as well?">
            <option value="targets">Only target PSMs</option>
            <option value="decoys">Both target and decoy PSMs</option>
        </param>
        <param argument="-tda" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Search with on-the-fly decoy database?" help="MSGF+ uses XXX_ as an accession prefix to indicate a decoy hit" />
        <param argument="-t" type="float" value="10" label="Precursor mass tolerance" help="Error tolerance for matching peptide mass to precursor ion mass"/>
        <param name="precursor_ion_tol_units" type="select" label="Precursor mass tolerance units" help="Daltons are common for low-res instruments, ppm for high-res instruments">
            <option value="ppm" selected="true">Parts per million (ppm)</option>
            <option value="Da">Daltons</option>

        </test>
        <test>
            <param name="msgf_input|intype_selector" value="single" />
            <param name="msgf_input|s" value="input/201208-378803.mzML" />
            <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" />
            <param name="tsv" value="decoys" />
            <param name="tda" value="1" />
            <param name="ntt" value="1" />
            <param name="t" value="50" />
            <param name="precursor_ion_tol_units" value="ppm" />
            <param name="common_fixed_modifications" value="" />