comparison msgfplus.xml @ 6:4b7d768b74d3 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 11837caf01413f2657b529b7cd7a4ec0960110fa

5:ce4882b95b73

<tool id="msgfplus" name="MS-GF+" version="0.3">
    <description>
        Identifies peptides in tandem mass spectra using the MS-GF+ search engine.
    </description>
    <requirements>
        <requirement type="package" version="2016.10.26">msgf_plus</requirement>

        #for $mod in $common_mods.split(",")
          echo '$mod.replace("_", ",")' >> Mods.txt &&
        #end for

        #for $mod in $custom_mods
          echo '${mod.formula_or_mass},${mod.aa_specificity},${mod.fix_or_opt},${mod.position_specificity},${mod.mod_name}' >> Mods.txt &&
        #end for

	msgf_plus
            -s '$input_name'
            -d '$db_name'
            -thread \${GALAXY_SLOTS:-1}
            -mod Mods.txt
            -tda $tda

            -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>
    <inputs>
        <conditional name="msgf_input">
          <param name="intype_selector" type="select" label="Type of MSGF+ analysis">
            <option value="single">Single database</option>
            <option value="fractions">Prefractionated database</option>
          </param>
          <when value="single">
            <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/>
            <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/>
          </when>
          <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">

            <param name="custom_mods_1|formula_or_mass" value="C10H10N5O7P" />
            <param name="custom_mods_1|aa_specificity" value="C,S" />
            <param name="custom_mods_1|fix_or_opt" value="opt" />
            <param name="custom_mods_1|position_specificity" value="any" />
            <param name="custom_mods_1|mod_name" value="cGMP" />

            <output name="output" file="201208-378803-msgf_20161026-2mmu-tryptic-many_mods.mzid" lines_diff="6" />
        </test>
    </tests>
    <help>
**What it does**

6:4b7d768b74d3

<tool id="msgfplus" name="MS-GF+" version="0.3.1">
    <description>
        Identifies peptides in tandem mass spectra using the MS-GF+ search engine.
    </description>
    <requirements>
        <requirement type="package" version="2016.10.26">msgf_plus</requirement>

        #for $mod in $common_mods.split(",")
          echo '$mod.replace("_", ",")' >> Mods.txt &&
        #end for

        #for $mod in $custom_mods
          #set aa_nocomma = str($mod.aa_specificity).replace(",", "")
          echo '${mod.formula_or_mass},${aa_nocomma},${mod.fix_or_opt},${mod.position_specificity},${mod.mod_name}' >> Mods.txt &&
        #end for

        msgf_plus
            -s '$input_name'
            -d '$db_name'
            -thread \${GALAXY_SLOTS:-1}
            -mod Mods.txt
            -tda $tda

            -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>
    <inputs>
        <conditional name="msgf_input">
            <param name="intype_selector" type="select" label="Type of MSGF+ analysis">
                <option value="single">Single database</option>
                <option value="fractions">Prefractionated database</option>
            </param>
            <when value="single">
                <param argument="-s" type="data" format="mzml" label="Input Raw MS File(s)"/>
                <param argument="-d" type="data" format="fasta" label="Protein Database" help="Select FASTA database from history"/>
              </when>
              <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">

            <param name="custom_mods_1|formula_or_mass" value="C10H10N5O7P" />
            <param name="custom_mods_1|aa_specificity" value="C,S" />
            <param name="custom_mods_1|fix_or_opt" value="opt" />
            <param name="custom_mods_1|position_specificity" value="any" />
            <param name="custom_mods_1|mod_name" value="cGMP" />
            
            <output name="output">
                <assert_contents>
                    <has_text text="iTRAQ4plex" />
                    <has_text text="pyro-Glu" />
                    <has_text text="Gly-loss" />
                    <has_text text="cGMP" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
**What it does**