6
+ − 1 <tool id="xcms_differential_analysis" name="XCMS Differential Analsysis" version="0.0.4">
+ − 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 $xsetData
+ − 9 "$class1"
+ − 10 "$class2"
+ − 11 $topcount
+ − 12 $outTable
+ − 13 $htmlReportFile
+ − 14 $htmlReportFile.files_path
+ − 15 $outLogFile
+ − 16 </command>
+ − 17 <inputs>
+ − 18
+ − 19 <param name="xsetData" type="data" format="rdata" label="xset xcms data file" help="E.g. output data file resulting from METAMS run"/>
+ − 20
+ − 21
+ − 22 <param name="class1" type="text" size="30" label="Class1 name" value="" help="Name of first class for the comparison"/>
+ − 23 <param name="class2" type="text" size="30" label="Class2 name" value="" help="Name of second class for the comparison"/>
+ − 24
+ − 25 <param name="topcount" type="integer" size="10" value="10" label="Number of items to return" help="Top X differential items. E.g. if 10, it will return top 10 differential items." />
+ − 26
+ − 27 </inputs>
+ − 28 <outputs>
+ − 29 <data name="outTable" format="tabular" label="${tool.name} on ${on_string} - Top differential items (TSV)"/>
+ − 30 <data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - log (LOG)" hidden="True"/>
+ − 31 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - differential report (HTML)"/>
+ − 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>