Mercurial > repos > lecorguille > xcms_summary

annotate abims_xcms_summary.xml @ 10:420f42a57916 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
author lecorguille
date Wed, 06 Jul 2016 17:43:46 -0400
parents ed8d80fc927c
children cb599006715f
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420f42a57916 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
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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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8
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9 <requirements>
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10 <requirement type="package" version="3.1.2">R</requirement>
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11 <requirement type="package" version="1.22.0">bioconductor-camera</requirement>
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12 <requirement type="package" version="1.1_4">r-batch</requirement>
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13 </requirements>
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15 <expand macro="stdio"/>
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16
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17 <command><![CDATA[
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18 $__tool_directory__/xcms_summary.r
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19
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20 image $image
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21 htmlOutput $htmlOutput
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22 user_email $__user_email__
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23
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24 ]]></command>
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25
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26 <inputs>
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28 <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
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30 </inputs>
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32 <outputs>
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33 <data name="htmlOutput" format="html" label="xcms summary html" />
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34 </outputs>
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36 <tests>
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37 <test>
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38 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" />
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39 <output name="htmlOutput" file="summary.html" />
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40 </test>
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41 </tests>
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43 <help><![CDATA[
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45 @HELP_AUTHORS@
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46
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47 ============
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48 Xcms.summary
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49 ============
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51 -----------
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52 Description
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53 -----------
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54
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55 This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools
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58 ---------------------------------------------------
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59
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60 Changelog/News
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61 --------------
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62
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63 **Version 1.0.2 - 06/07/2016**
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65 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
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67 **Version 1.0.1 - 04/04/2016**
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69 - TEST: refactoring to pass planemo test using conda dependencies
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71
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72 **Version 1.0.0 - 10/02/2016**
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74 - NEW: Create a summary of XCMS analysis
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77 ]]></help>
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80 <expand macro="citation" />
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82 </tool>