Mercurial > repos > lecorguille > xcms_summary

annotate abims_xcms_summary.xml @ 11:cb599006715f draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
author lecorguille
date Mon, 30 Jan 2017 08:54:06 -0500
parents 420f42a57916
children 27e7da5f6848
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1 <tool id="abims_xcms_summary" name="xcms.summary" version="1.0.2">
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3 <description>Create a summary of XCMS analysis</description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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9 <requirements>
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10 <requirement type="package" version="1.26.0">bioconductor-camera</requirement>
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11 <requirement type="package" version="1.1_4">r-batch</requirement>
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12 </requirements>
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14 <expand macro="stdio"/>
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16 <command><![CDATA[
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17 $__tool_directory__/xcms_summary.r
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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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23 ]]></command>
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25 <inputs>
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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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29 </inputs>
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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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35 <tests>
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36 <test>
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37 <param name="image" value="faahKO.xset.group.retcor.group.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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44 @HELP_AUTHORS@
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45
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46 ============
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47 Xcms.summary
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48 ============
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50 -----------
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51 Description
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52 -----------
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53
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54 This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools
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57 ---------------------------------------------------
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59 Changelog/News
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60 --------------
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61
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62 **Version 1.0.2 - 06/07/2016**
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64 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
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66 **Version 1.0.1 - 04/04/2016**
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68 - TEST: refactoring to pass planemo test using conda dependencies
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70
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71 **Version 1.0.0 - 10/02/2016**
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73 - NEW: Create a summary of XCMS analysis
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76 ]]></help>
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79 <expand macro="citation" />
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81 </tool>