Mercurial > repos > pieterlukasse > prims_metabolomics
view xcms_differential_analysis.xml @ 49:f772a5caa86a
Added more options and better documentation.
Added MsClust support for parsing XCMS alignment results.
Improved output reports for XCMS wrappers.
New tools.
author | pieter.lukasse@wur.nl |
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date | Wed, 10 Dec 2014 22:03:27 +0100 |
parents | e67149fbff20 |
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<tool id="xcms_differential_analysis" name="XCMS Differential Analsysis" version="0.0.4"> <description> Runs xcms diffreport function for differential Analsysis</description> <requirements> <requirement type="package" version="3.1.1">R_bioc_metams</requirement> </requirements> <command interpreter="Rscript"> xcms_differential_analysis.r $xsetData "$class1" "$class2" $topcount $outTable $htmlReportFile $htmlReportFile.files_path $outLogFile </command> <inputs> <param name="xsetData" type="data" format="rdata" label="xset xcms data file" help="E.g. output data file resulting from METAMS run"/> <param name="class1" type="text" size="30" label="Class1 name" value="" help="Name of first class for the comparison"/> <param name="class2" type="text" size="30" label="Class2 name" value="" help="Name of second class for the comparison"/> <param name="topcount" type="integer" size="10" value="10" label="Number of items to return" help="Top X differential items. E.g. if 10, it will return top 10 differential items." /> </inputs> <outputs> <data name="outTable" format="tabular" label="${tool.name} on ${on_string} - Top differential items (TSV)"/> <data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - log (LOG)" hidden="True"/> <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - differential report (HTML)"/> </outputs> <tests> <test> </test> </tests> <help> .. class:: infomark Runs xcms diffreport for showing the most significant differences between two sets/classes of samples. This tool also creates extracted ion chromatograms (EICs) for the most significant differences. The figure below shows an example of such an EIC. .. image:: $PATH_TO_IMAGES/diffreport.png </help> <citations> <citation type="doi">10.1021/ac051437y</citation> <!-- example see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set --> </citations> </tool>