Mercurial > repos > pieterlukasse > prims_metabolomics
comparison 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 |
|---|---|
| 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> |