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