comparison msgfplus.xml @ 4:58f9cf0de6d4 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b2712071afd2d74261bc3e3fc555355f5675a0d6

3:b4ccaf21855d

<tool id="msgfplus" name="MS-GF+" version="0.1">
    <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>

    </stdio>
    <command>

<![CDATA[
        #if $msgf_input.intype_selector == "single"
        #set $db_name = $msgf_input.d.display_name.replace(".fasta", "") + ".fasta"
        #set $input_name = $msgf_input.s.display_name
        ln -s '$msgf_input.s' '${input_name}' &&
        ln -s '$msgf_input.d' '${db_name}' &&
        #else if $msgf_input.intype_selector == "fractions"
        #set $db_name = $msgf_input.db_spectra.reverse.display_name.replace(".fasta", "") + ".fasta"
        #set $input_name = $msgf_input.db_spectra.forward.display_name
        ln -s '$msgf_input.db_spectra.forward' '${input_name}' &&
        ln -s '$msgf_input.db_spectra.reverse' '${db_name}' &&
        #end if
        #set $output_name = $input_name.replace(".mzML", "") + ".mzid"

        echo \\#Mods > Mods.txt &&
        #set $common_mods = str($common_fixed_modifications) + "," + str($common_variable_modifications)
        #for $mod in $common_mods.split(",")
          echo '$mod.replace("_", ",")' >> Mods.txt &&

            <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 FASTA database (forward) and spectra (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="ntt" value="1" />
            <param name="t" value="50" />
            <param name="precursor_ion_tol_units" value="ppm" />            
            <param name="common_fixed_modifications" value="" />
            <param name="common_variable_modifications" value="" />
            <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="20" />
        </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" />

4:58f9cf0de6d4

<tool id="msgfplus" name="MS-GF+" version="0.2">
    <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>

    </stdio>
    <command>

<![CDATA[
        #if $msgf_input.intype_selector == "single"
        #set $db_name = $msgf_input.d.element_identifier.replace(".fasta", "") + ".fasta"
        #set $input_name = $msgf_input.s.element_identifier.replace(".mzML", "") + ".mzML"
        ln -s '$msgf_input.s' '${input_name}' &&
        ln -s '$msgf_input.d' '${db_name}' &&
        #else if $msgf_input.intype_selector == "fractions"
        #set $db_name = $msgf_input.db_spectra.reverse.element_identifier.replace(".fasta", "") + ".fasta"
        #set $input_name = $msgf_input.db_spectra.forward.element_identifier.replace(".mzML", "") + ".mzML"
        ln -s '$msgf_input.db_spectra.forward' '${input_name}' &&
        ln -s '$msgf_input.db_spectra.reverse' '${db_name}' &&
        #end if
        #set $output_name = $input_name.replace(".mzML", ".mzid")

        echo \\#Mods > Mods.txt &&
        #set $common_mods = str($common_fixed_modifications) + "," + str($common_variable_modifications)
        #for $mod in $common_mods.split(",")
          echo '$mod.replace("_", ",")' >> Mods.txt &&

            <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="ntt" value="1" />
            <param name="t" value="50" />
            <param name="precursor_ion_tol_units" value="ppm" />            
            <param name="common_fixed_modifications" value="" />
            <param name="common_variable_modifications" value="" />
            <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="100" />
        </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" />