Mercurial > repos > jjohnson > spectrast2spectrast_irt
view spectrast2spectrast_irt.xml @ 1:dc40297705fc draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt commit 616f0282d3a3e0b433c324e899bea7b0dcd3d7e0-dirty
author | jjohnson |
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date | Thu, 26 Jul 2018 10:53:48 -0400 |
parents | 90dcbb52c83a |
children | f5ca880950f7 |
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<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 ${input.extra_files_path}/library.sptxt --out outdir/library.splib #if str($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>