view spectrast2spectrast_irt.xml @ 3:c45a03486b3a draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt commit cf45d340518a13e8048c817aa8a61412c5e886db-dirty

<tool id="gp_spectrast2spectrast_irt" name="SpectraST RT Normalizer" version="0.5.0">
    <description></description>
    <requirements>
        <requirement type="package" version="0.5.0">msproteomicstools</requirement>
    </requirements>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <!-- In case the return code has not been set propery check stderr too -->
        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>
    <command>
<![CDATA[
        ## may have to link splib
        mkdir -p outdir &&
        spectrast2spectrast_irt.py
            --in ${input.extra_files_path}/library.sptxt
            --out outdir/library.splib
            #if i$kits.src == 'biognosys_irt':
                #if str($kits.kit) != 'None':
                    --kit "#echo ",".join(str($kits.kit).split(','))#"
                #end if
            #elif $kits.src == 'history':
                #set $pep_irts = []
                #for line in open($kits.irt_file,'r').readlines():
                    #silent $pep_irts.append(':'.join(line.strip().split('\t')))
                #end for
                --kit "#echo ",".join($pep_irts)#"
            #end if
            $applychauvenet
            $precursorlevel
            $spectralevel
            $report
            ##--exclude $exclude
            ##--surrogate $surrogate
            ##--linearregression $linearregression
            --rsq_threshold $rsq_threshold &&
         cp -p outdir/library.splib outdir/library.sptxt &&
        mkdir -p '$output.files_path' &&
        for i in library.splib library.sptxt library.spidx library.pepidx; do if [ -e outdir/\${i} ]; then cp -p outdir/\${i} '$output.files_path'; fi; done
]]>
    </command>
    <inputs>
        <param name="input" format="splib" type="data" label="Spectrast files" help="" />

        <param name="applychauvenet" type="boolean" truevalue="--applychauvenet" falsevalue="" checked="False"
            label="Use Chavenet's criterion to exclude outliers" help="(--applychauvenet)" />

        <param name="precursorlevel" type="boolean" truevalue="--precursorlevel" falsevalue="" checked="False"
            label="Use precursors instead of peptides for grouping" help="(--precursorlevel)" />

        <param name="spectralevel" type="boolean" truevalue="--spectralevel" falsevalue="" checked="False"
            label="Do not merge or group any peptides or precursors" help="Use raw spectra. (--spectralevel)" />

        <param name="report" type="boolean" truevalue="--report" falsevalue="" checked="False"
            label="Create a report CSV file" help="(--report)" />

        <param name="rsq_threshold" type="float" value="0.95" label="Specify r-squared threshold to accept linear regression" help="(--rsq_threshold)" />

        <conditional name="kits">
            <param name="src" type="select" label="iRT kit selection">
                <option value="biognosys_irt">Biognosys iRT</option>
                <option value="history">History dataset (2 columns: peptide iRT)</option>
            </param>
            <when value="biognosys_irt">
                <param name="kit" type="select" multiple="True" optional="True" label="Specifiy RT-kit">
                    <option value="LGGNEQVTR:-28.3083">LGGNEQVTR:-28.3083</option>
                    <option value="GAGSSEPVTGLDAK:0.227424">GAGSSEPVTGLDAK:0.227424</option>
                    <option value="VEATFGVDESNAK:13.1078">VEATFGVDESNAK:13.1078</option>
                    <option value="YILAGVENSK:22.3798">YILAGVENSK:22.3798</option>
                    <option value="TPVISGGPYEYR:28.9999">TPVISGGPYEYR:28.9999</option>
                    <option value="TPVITGAPYEYR:33.6311">TPVITGAPYEYR:33.6311</option>
                    <option value="DGLDAASYYAPVR:43.2819">DGLDAASYYAPVR:43.2819</option>
                    <option value="ADVTPADFSEWSK:54.969">ADVTPADFSEWSK:54.969</option>
                    <option value="GTFIIDPGGVIR:71.3819">GTFIIDPGGVIR:71.3819</option>
                    <option value="GTFIIDPAAVIR:86.7152">GTFIIDPAAVIR:86.7152</option>
                    <option value="LFLQFGAQGSPFLK:98.0897">LFLQFGAQGSPFLK:98.0897</option>
                </param>
            </when>
            <when value="history">
                <param name="irt_file" type="data" format="tabular" label="Peptide iRT table" 
                   help="2 columns: peptide iRT" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_report" format="csv" from_work_dir="outdir/library.csv">
            <filter>report</filter>
        </data>
        <data name="output" format="splib"/>
    </outputs>
    <tests>
        <!--
        <test>
            <param name="input" value="HEK_Lib_7Nov13.splib" ftype="txt" />
            <param name="report" value="True" />
            <output name="output_splib" file="spectrast2spectrast_irt_output_1_splib.txt" ftype="txt" />
            <output name="output_pepidx" file="spectrast2spectrast_irt_output_1_pepids.txt" ftype="txt" />
            <output name="output_report" file="spectrast2spectrast_irt_output_1_report.txt" ftype="txt" />
        </test>
        <test>
            <param name="input" value="HEK_Lib_7Nov13.splib" ftype="txt" />
            <param name="report" value="False" />
            <param name="kit" value="LGGNEQVTR:-28.3083,GAGSSEPVTGLDAK:0.227424" />
            <output name="output_splib" file="spectrast2spectrast_irt_output_2_splib.txt" ftype="txt" />
            <output name="output_pepidx" file="spectrast2spectrast_irt_output_2_pepids.txt" ftype="txt" />
        </test>
        -->
    </tests>
  <help>
<![CDATA[
**What it does**

SpectraST RT Normalizer
---------------------------------------------------------------------------------------------
Usage:     spectrast2spectrast_irt.py -i non_consensus_library.[splib/sptxt] -o non_consensus_library_irt.splib
Input:     SpectraST non_consensus_library.splib in txt format
Output:    SpectraST non_consensus_library_irt.[splib/pepidx] and regression plots for all runs.
Argument:  -i [--in]: input file
           -o [--out]: output file
           (optional) -k [--kit]: specifiy RT-kit [LGGNEQVTR:-28.3083,GAGSSEPVTGLDAK:0.227424,VEATFGVDESNAK:13.1078,YILAGVENSK:22.3798,TPVISGGPYEYR:28.9999,TPVITGAPYEYR:33.6311,DGLDAASYYAPVR:43.2819,ADVTPADFSEWSK:54.969,GTFIIDPGGVIR:71.3819,GTFIIDPAAVIR:86.7152,LFLQFGAQGSPFLK:98.0897]
           (optional) -a [--applychauvenet]: should Chavenet's criterion be used to exclude outliers?
           (optional) -p [--precursorlevel]: should precursors instead of peptides be used for grouping?
           (optional)    [--spectralevel]: do not merge or group any peptides or precursors (use raw spectra)
           (optional) -r [--report]: should a csv report be written?
           (optional) -e [--exclude]: specify peptides from the RT-kit to exclude [run_id1:LGGNEQVTR,run_id2:GAGSSEPVTGLDAK]
           (optional) -s [--surrogate]: specify surrogate calibrations [broken_run_id1:working_run_id2]
           (optional) -l [--linearregression]: specify surrogate linear regressions (first number: c, second number: m) [broken_run_id1:1/3]
           (optional) -t [--rsq_threshold]: specify r-squared threshold to accept linear regression [0.95]
Important: The splib need to be in txt format!
           spectrast -c_BIN! -cNnon_consensus.txt non_consensus.bin.splib
           All runs in your library further need to contain the Biognosys RT-kit peptides.
Contact:   George Rosenberger <[e-mail]>



]]>
    </help>
    <citations>
    </citations>
</tool>