comparison msgfplus.xml @ 3:b4ccaf21855d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit 498437250b9fa438abd6865b7e9ba71298599ee7

2:058a2ab1d462

    <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>
        <environment_variable name="LC_ALL" action="set_to">C</environment_variable>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Job Failed" />
        <regex match="java.*Exception" level="fatal" description="Java Exception"/> 
        <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>

            -maxLength $advanced.maxLength
            -minCharge $advanced.minCharge
            -maxCharge $advanced.maxCharge
            -n $advanced.n
            -addFeatures $advanced.addFeatures
        &&
        mv '$output_name' output
]]>
    </command>
    <inputs>

          <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 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>

            <param name="isotope_high" label="Upper isotope error range" type="integer" value="1" /> 
        </section>
    </inputs>
    <outputs>
        <data name="output" format="mzid" from_work_dir="output" />
    </outputs>
    <tests>
        <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="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="" />
            <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="fractions" />
            <param name="msgf_input.db_spectra.forward" value="input/201208-378803.mzML" />
            <param name="msgf_input.db_spectra.reverse" value="input/cow.protein.PRG2012-subset.fasta" />
            <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="" />
            <param name="common_variable_modifications" value="" />
            <output name="output" file="201208-378803-msgf-50ppm-semitryptic-no_mods.mzid" lines_diff="6" />
        </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="tda" value="1" />
            <param name="t" value="0.02" />
            <param name="precursor_ion_tol_units" value="Da" />
            <param name="isotope_low" value="-1" />
            <param name="isotope_high" value="0" />

3:b4ccaf21855d

    <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>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Job Failed" />
        <regex match="java.*Exception" level="fatal" description="Java Exception"/> 
        <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>

            -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>

          <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="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>

            <param name="isotope_high" label="Upper isotope error range" type="integer" value="1" /> 
        </section>
    </inputs>
    <outputs>
        <data name="output" format="mzid" from_work_dir="output" />
        <data name="tsvoutput" format="tabular" from_work_dir="output.tsv" >
          <filter>tsvcheck</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="msgf_input|intype_selector" value="single" />
            <param name="msgf_input|s" value="input/201208-378803.mzML" ftype="mzml" />
            <param name="msgf_input|d" value="input/cow.protein.PRG2012-subset.fasta" ftype="fasta" />
            <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="" />
            <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" />
            <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="" />
            <param name="common_variable_modifications" value="" />
            <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="20" />
            <output name="tsvoutput" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.tsv" compare="sim_size" delta="20" />
        </test>
        <test>
            <param name="msgf_input|intype_selector" value="fractions" />
            <param name="msgf_input|db_spectra">
                <collection type="paired">
                    <element name="forward" value="input/201208-378803.mzML" />
                    <element name="reverse" value="input/cow.protein.PRG2012-subset.fasta" />
                </collection>
            </param>
            <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="" />
            <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" />
            <param name="tda" value="1" />
            <param name="t" value="0.02" />
            <param name="precursor_ion_tol_units" value="Da" />
            <param name="isotope_low" value="-1" />
            <param name="isotope_high" value="0" />