comparison spectrast2spectrast_irt.xml @ 0:90dcbb52c83a draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt commit 225dd7d91b12108dd3a4eec00e45771ec8127259-dirty

0:90dcbb52c83a

<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 ${input.extra_file_path}/library.sptxt
            --out outdir/library.splib
            #if str($kit) != 'None':
                --kit "#echo ",".join(str($kit).split(','))#"
            #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)" />

        <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>
    </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**

Filter from spectraST files to swath input files.


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