Mercurial > repos > pieterlukasse > prims_metabolomics

comparison xcms_differential_analysis.xml @ 49:f772a5caa86a

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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
date Wed, 10 Dec 2014 22:03:27 +0100
parents e67149fbff20
children
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48:26b93438f30e 49:f772a5caa86a
1 <tool id="xcms_differential_analysis" name="XCMS Differential Analsysis" version="0.0.1"> 1 <tool id="xcms_differential_analysis" name="XCMS Differential Analsysis" version="0.0.4">
2 <description> Runs xcms diffreport function for differential Analsysis</description> 2 <description> Runs xcms diffreport function for differential Analsysis</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.1.1">R_bioc_metams</requirement> 4 <requirement type="package" version="3.1.1">R_bioc_metams</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="Rscript"> 6 <command interpreter="Rscript">
7 xcms_differential_analysis.r 7 xcms_differential_analysis.r
8 $xsetData 8 $xsetData
9 $class1 9 "$class1"
10 $class2 10 "$class2"
11 $topcount 11 $topcount
12 $outTable 12 $outTable
13 $outLogFile
14 $htmlReportFile 13 $htmlReportFile
15 $htmlReportFile.files_path 14 $htmlReportFile.files_path
15 $outLogFile
16 </command> 16 </command>
17 <inputs> 17 <inputs>
18 18
19 <param name="xsetData" type="data" format="rdata" label="xset xcms data file" help="E.g. output data file resulting from METAMS run"/> 19 <param name="xsetData" type="data" format="rdata" label="xset xcms data file" help="E.g. output data file resulting from METAMS run"/>
20 20
25 <param name="topcount" type="integer" size="10" value="10" label="Number of items to return" help="Top X differential items. E.g. if 10, it will return top 10 differential items." /> 25 <param name="topcount" type="integer" size="10" value="10" label="Number of items to return" help="Top X differential items. E.g. if 10, it will return top 10 differential items." />
26 26
27 </inputs> 27 </inputs>
28 <outputs> 28 <outputs>
29 <data name="outTable" format="tabular" label="${tool.name} on ${on_string} - Top differential items (TSV)"/> 29 <data name="outTable" format="tabular" label="${tool.name} on ${on_string} - Top differential items (TSV)"/>
30 <data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - differential log (LOG)"/> 30 <data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - log (LOG)" hidden="True"/>
31 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - differential report (HTML)"/> 31 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - differential report (HTML)"/>
32 </outputs> 32 </outputs>
33 <tests> 33 <tests>
34 <test> 34 <test>
35 </test> 35 </test>