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annotate abims_xcms_report.xml @ 5:2fd29f68d90e draft

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author lecorguille
date Wed, 23 Dec 2015 09:30:33 -0500
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1 <tool id="abims_xcms_report" name="xcms.report" version="0.1.0">
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3 <description>Create a report of XCMS analysis</description>
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5 <requirements>
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6 <requirement type="package" version="3.1.2">R</requirement>
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7 <requirement type="binary">Rscript</requirement>
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8 <requirement type="package" version="1.44.0">xcms</requirement>
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9 </requirements>
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11 <stdio>
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12 <exit_code range="1:" level="fatal" />
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13 </stdio>
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15 <command interpreter="Rscript"><![CDATA[
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16 xcms_report.r
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18 image $image
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19 htmlOutput $htmlOutput
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20 user_email $__user_email__
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22 ]]></command>
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24 <inputs>
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26 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, group, retcor, fillpeaks etc.)" />
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28 </inputs>
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30 <outputs>
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31 <data name="htmlOutput" format="html" label="xcms report html" />
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32 </outputs>
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33
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34 <tests>
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35 <test>
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36 <param name="image" value="fillpeaks.RData" />
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37 <output name="htmlOutput" file="report.html" />
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38 </test>
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39 </tests>
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40
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41 <help><![CDATA[
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42
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43 .. class:: infomark
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44
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45 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff part of Workflow4Metabolomics.org [W4M]
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47 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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49 ---------------------------------------------------
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51 ============
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52 Xcms.report
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53 ============
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54
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55 -----------
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56 Description
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57 -----------
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58
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59 This tool provide a HTML report which summarizes your analysis using the [W4M] XCMS and CAMERA tools
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62 ]]></help>
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65 <citations>
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66 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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67 </citations>
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68
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69 </tool>