Mercurial > repos > pieterlukasse > prims_metabolomics
annotate 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 |
| rev | line source |
|---|---|
|
49
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
41
diff
changeset
|
1 <tool id="xcms_differential_analysis" name="XCMS Differential Analsysis" version="0.0.4"> |
| 41 | 2 <description> Runs xcms diffreport function for differential Analsysis</description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="3.1.1">R_bioc_metams</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="Rscript"> | |
| 7 xcms_differential_analysis.r | |
| 8 $xsetData | |
|
49
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
41
diff
changeset
|
9 "$class1" |
|
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
41
diff
changeset
|
10 "$class2" |
| 41 | 11 $topcount |
| 12 $outTable | |
| 13 $htmlReportFile | |
| 14 $htmlReportFile.files_path | |
|
49
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
41
diff
changeset
|
15 $outLogFile |
| 41 | 16 </command> |
| 17 <inputs> | |
| 18 | |
| 19 <param name="xsetData" type="data" format="rdata" label="xset xcms data file" help="E.g. output data file resulting from METAMS run"/> | |
| 20 | |
| 21 | |
| 22 <param name="class1" type="text" size="30" label="Class1 name" value="" help="Name of first class for the comparison"/> | |
| 23 <param name="class2" type="text" size="30" label="Class2 name" value="" help="Name of second class for the comparison"/> | |
| 24 | |
| 25 <param name="topcount" type="integer" size="10" value="10" label="Number of items to return" help="Top X differential items. E.g. if 10, it will return top 10 differential items." /> | |
| 26 | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <data name="outTable" format="tabular" label="${tool.name} on ${on_string} - Top differential items (TSV)"/> | |
|
49
f772a5caa86a
Added more options and better documentation.
pieter.lukasse@wur.nl
parents:
41
diff
changeset
|
30 <data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - log (LOG)" hidden="True"/> |
| 41 | 31 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - differential report (HTML)"/> |
| 32 </outputs> | |
| 33 <tests> | |
| 34 <test> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help> | |
| 38 | |
| 39 .. class:: infomark | |
| 40 | |
| 41 Runs xcms diffreport for showing the most significant differences between two sets/classes of samples. This tool also creates extracted ion chromatograms (EICs) for | |
| 42 the most significant differences. The figure below shows an example of such an EIC. | |
| 43 | |
| 44 .. image:: $PATH_TO_IMAGES/diffreport.png | |
| 45 | |
| 46 | |
| 47 | |
| 48 | |
| 49 </help> | |
| 50 <citations> | |
| 51 <citation type="doi">10.1021/ac051437y</citation> <!-- example | |
| 52 see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set | |
| 53 --> | |
| 54 </citations> | |
| 55 </tool> |