Mercurial > repos > lecorguille > xcms_summary

annotate abims_xcms_summary.xml @ 26:e6a6503d7d6d draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 392e432529877680e80a7b338e20d69a42e53767-dirty
author lecorguille
date Mon, 03 Apr 2017 07:56:40 -0400
parents 3a53e63555c7
children 33694028a409
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1 <tool id="abims_xcms_summary" name="xcms.summary" version="1.0.3">
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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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34
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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="faahKO.xset.group.retcor.group.fillpeaks.summary.html" />
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39 </test>
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40 <test>
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41 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" />
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42 <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" />
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43 </test>
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44 </tests>
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45
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46 <help><![CDATA[
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48 @HELP_AUTHORS@
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49
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50 ============
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51 Xcms.summary
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52 ============
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53
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54 -----------
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55 Description
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56 -----------
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57
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58 This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools
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60 -----------------
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61 Workflow position
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62 -----------------
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64 **Upstream tools**
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66 ========================= ================= ===================== ==========
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67 Name output file format parameter
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68 ========================= ================= ===================== ==========
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69 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
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70 ------------------------- ----------------- --------------------- ----------
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71 xcms.group xset.RData rdata.xcms.group RData file
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72 ------------------------- ----------------- --------------------- ----------
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73 xcms.retcor xset.RData rdata.xcms.retcor RData file
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74 ------------------------- ----------------- --------------------- ----------
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75 xcms.fillpeaks xset.RData rdata.xcms.fillpeaks RData file
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76 ------------------------- ----------------- --------------------- ----------
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77 CAMERA.annotate xset.RData rdata.camera.* RData file
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78 ========================= ================= ===================== ==========
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81 .. image:: xcms_summary_workflow.png
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83 ---------------------------------------------------
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84
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85 Changelog/News
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86 --------------
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87
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88 **Version 1.0.3 - 03/02/2017**
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90 - IMPROVEMENT: xcms.summary can deal with merged individual data
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92 **Version 1.0.2 - 06/07/2016**
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94 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
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95
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96 **Version 1.0.1 - 04/04/2016**
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98 - TEST: refactoring to pass planemo test using conda dependencies
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100
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101 **Version 1.0.0 - 10/02/2016**
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102
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103 - NEW: Create a summary of XCMS analysis
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105
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106 ]]></help>
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107
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109 <expand macro="citation" />
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110
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111 </tool>