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1 <tool id="abims_xcms_summary" name="xcms.summary" version="1.0.0">
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2
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3 <description>Create a summary of XCMS analysis</description>
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4
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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 <requirement type="package" version="1.22.0">camera</requirement>
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10 </requirements>
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11
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12 <stdio>
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13 <exit_code range="1:" level="fatal" />
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14 </stdio>
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15
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16 <command interpreter="Rscript"><![CDATA[
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17 xcms_summary.r
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18
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19 image $image
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20 htmlOutput $htmlOutput
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21 user_email $__user_email__
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22
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23 ]]></command>
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24
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25 <inputs>
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26
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27 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, group, retcor, fillpeaks etc.)" />
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28
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29 </inputs>
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30
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31 <outputs>
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32 <data name="htmlOutput" format="html" label="xcms summary html" />
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33 </outputs>
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34
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35 <tests>
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36 <test>
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37 <param name="image" value="fillpeaks.RData" />
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38 <output name="htmlOutput" file="summary.html" />
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39 </test>
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40 </tests>
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41
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42 <help><![CDATA[
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43
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44 .. class:: infomark
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45
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46 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff part of Workflow4Metabolomics.org [W4M]
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47
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48 | 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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50 ---------------------------------------------------
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51
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52 ============
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53 Xcms.summary
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54 ============
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55
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56 -----------
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57 Description
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58 -----------
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59
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60 This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools
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61
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62
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63 ---------------------------------------------------
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64
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65 Changelog/News
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66 --------------
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67
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68 **Version 1.0.0 - 10/02/2016**
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69
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70 - NEW: Create a summary of XCMS analysis
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71
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72
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73 ]]></help>
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74
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75
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76 <citations>
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77 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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78 </citations>
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79
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80 </tool>
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