comparison pepquery2.xml @ 2:c32806a80862 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 22916ed24dfb8452c8142e5d6b282d0e931af91f

1:b5489f81c2fa

                <option value="novel" selected="true">novel peptide/protein validation</option>
                <option value="known">known peptide/protein validation</option>
            </param>
            <when value="novel"/> 
            <when value="known"> 
                 <param name="decoy" argument="-decoy" type="boolean" truevalue="-decoy" falsevalue="" checked="false" label="Identity the decoy version of the selected target protein"/>
            </when>
        </conditional>
        <section name="req_inputs" title="Input Data" expanded="true">
            <conditional name="input_type">
                <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" >

                    <option value="indexed">Indexed MS/MS spectrums</option>
                    <option value="PepQueryDB">PepQueryDB</option>
                    <option value="public">public proteomics data repositories</option>
                </param>
                <when value="history">
                    <param name="spectrum_files" argument="-ms" type="data" format="mgf,mzml,mzxml,thermo.raw" label="Spectrum File" help="Spectrum file used for identification, formats: MGF,mzML,mzXML,Thermo RAW" />
                </when>
                <when value="indexed">
                    <param name="index" argument="-ms" type="data" format="txt" label="PepQuery Index" help="" />
                </when>
                <when value="PepQueryDB">

                        <validator type="regex" message="An identifier strating with PXD or MSV or JPST">^(PXD|MSV|JPST).*$</validator>
                    </param>
                </when>
            </conditional>

            <param name="indexType" argument="-indexType" type="select" optional="true" label="Report Spectrum Scan as" help="Default: index" >
                <option value="1">index (1-based) in MGF</option>
                <option value="2">spectrum title in MGF</option>
            </param>
        </section>

                <expand macro="modifications" />
             </param>

             <param name="max_mods" argument="-maxVar" type="integer" label="Max Modifications" value="" min="0" max="10" optional="true" help="Max number of variable modifications  Default: 3" />
             <param name="unmodified" argument="-hc" type="boolean" truevalue="-hc" falsevalue="" checked="false" label="Use more stringent criterion for unrestricted modification searching" help="TRUE: score(UMS)>=score(targetPSM); FALSE: score(UMS)>score(targetPSM)" />
             <param name="aa" argument="-aa" type="boolean" truevalue="-aa" falsevalue="" checked="false" label="Consider amino acid substitution modifications?" help="Whether or not to consider aa substitution modifications when perform modification filtering." />
        </section>

        <section name="digestion" title="Digestion" expanded="false">
            <param name="enzyme" argument="-e" type="select" optional="true" label="Enzyme" help="Enzyme used for protein digestion.  Default: Trypsin" >
                <option value="0">Non enzyme</option>

            <option value="detail.txt">detail.txt</option>
            <option value="ptm.txt">ptm.txt</option>
            <option value="ptm_detail.txt">ptm_detail.txt</option>
            <option value="ms_index">MS/MS Index</option>
        </param>
        <param name="fast" argument="-fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Use fast mode for searching" help="In fast mode, only one better match from reference peptide-based competitive filtering steps will be returned. A peptide identified or not is not affected by this setting. For most applications, fast mode will speed up the analysis." />
    </inputs>
    <outputs>
        <data name="log_txt" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt">
        </data> 
        <data name="parameter_txt" format="txt" from_work_dir="pepquery_output/parameter.txt" label="${tool.name} on ${on_string}: parameter.txt">

2:c32806a80862

                <option value="novel" selected="true">novel peptide/protein validation</option>
                <option value="known">known peptide/protein validation</option>
            </param>
            <when value="novel"/> 
            <when value="known"> 
                 <param argument="-decoy" type="boolean" truevalue="-decoy" falsevalue="" checked="false" label="Identity the decoy version of the selected target protein"/>
            </when>
        </conditional>
        <section name="req_inputs" title="Input Data" expanded="true">
            <conditional name="input_type">
                <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" >

                    <option value="indexed">Indexed MS/MS spectrums</option>
                    <option value="PepQueryDB">PepQueryDB</option>
                    <option value="public">public proteomics data repositories</option>
                </param>
                <when value="history">
                    <param name="spectrum_files" argument="-ms" type="data" format="mgf,mzml,mzxml" label="Spectrum File" help="Spectrum file used for identification, formats: MGF,mzML,mzXML" />
                </when>
                <when value="indexed">
                    <param name="index" argument="-ms" type="data" format="txt" label="PepQuery Index" help="" />
                </when>
                <when value="PepQueryDB">

                        <validator type="regex" message="An identifier strating with PXD or MSV or JPST">^(PXD|MSV|JPST).*$</validator>
                    </param>
                </when>
            </conditional>

            <param argument="-indexType" type="select" optional="true" label="Report Spectrum Scan as" help="Default: index" >
                <option value="1">index (1-based) in MGF</option>
                <option value="2">spectrum title in MGF</option>
            </param>
        </section>

                <expand macro="modifications" />
             </param>

             <param name="max_mods" argument="-maxVar" type="integer" label="Max Modifications" value="" min="0" max="10" optional="true" help="Max number of variable modifications  Default: 3" />
             <param name="unmodified" argument="-hc" type="boolean" truevalue="-hc" falsevalue="" checked="false" label="Use more stringent criterion for unrestricted modification searching" help="TRUE: score(UMS)>=score(targetPSM); FALSE: score(UMS)>score(targetPSM)" />
             <param argument="-aa" type="boolean" truevalue="-aa" falsevalue="" checked="false" label="Consider amino acid substitution modifications?" help="Whether or not to consider aa substitution modifications when perform modification filtering." />
        </section>

        <section name="digestion" title="Digestion" expanded="false">
            <param name="enzyme" argument="-e" type="select" optional="true" label="Enzyme" help="Enzyme used for protein digestion.  Default: Trypsin" >
                <option value="0">Non enzyme</option>

            <option value="detail.txt">detail.txt</option>
            <option value="ptm.txt">ptm.txt</option>
            <option value="ptm_detail.txt">ptm_detail.txt</option>
            <option value="ms_index">MS/MS Index</option>
        </param>
        <param argument="-fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Use fast mode for searching" help="In fast mode, only one better match from reference peptide-based competitive filtering steps will be returned. A peptide identified or not is not affected by this setting. For most applications, fast mode will speed up the analysis." />
    </inputs>
    <outputs>
        <data name="log_txt" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt">
        </data> 
        <data name="parameter_txt" format="txt" from_work_dir="pepquery_output/parameter.txt" label="${tool.name} on ${on_string}: parameter.txt">