Mercurial > repos > lecorguille > xcms_summary

annotate abims_xcms_summary.xml @ 36:12c802da5367 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
author lecorguille
date Mon, 17 Sep 2018 08:47:17 -0400
parents 79fe34cedc56
children 1d2cc6c87acf
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1 <tool id="abims_xcms_summary" name="xcms process history" version="@WRAPPER_VERSION@.0">
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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 <import>macros_xcms.xml</import>
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8 </macros>
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10 <expand macro="requirements">
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11 <requirement type="package" version="1.32.0">bioconductor-camera</requirement>
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12 </expand>
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14 <expand macro="stdio"/>
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16 <command><![CDATA[
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17 @COMMAND_RSCRIPT@/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.findchrompeaks,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" ftype="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" ftype="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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46 <help><![CDATA[
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48 @HELP_AUTHORS@
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50 ====================
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51 xcms process history
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52 ====================
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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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65
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66 ========================= =========================== ================================
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67 Name Output file Format
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68 ========================= =========================== ================================
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69 xcms.findChromPeaks xset.RData rdata.xcms.findchrompeaks
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70 ------------------------- --------------------------- --------------------------------
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71 xcms.groupChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group
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72 ------------------------- --------------------------- --------------------------------
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73 xcms.adjustRtime ``*``.adjustRtime.RData rdata.xcms.retcor
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74 ------------------------- --------------------------- --------------------------------
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75 xcms.fillChromPeaks ``*``.fillChromPeaks.RData rdata.xcms.fillpeaks
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76 ------------------------- --------------------------- --------------------------------
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77 CAMERA.annotate ``*``.annotate.*.RData rdata.camera.``*``
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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 3.0.0.0 - 14/02/2018**
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89
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90 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods
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92 - IMPROVEMENT: the tool now shows all the parameters and not only those which were set.
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95 **Version 1.0.4 - 13/02/2018**
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97 - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0
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100 **Version 1.0.3 - 03/02/2017**
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102 - IMPROVEMENT: xcms.summary can deal with merged individual data
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105 **Version 1.0.2 - 06/07/2016**
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107 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
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110 **Version 1.0.1 - 04/04/2016**
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111
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112 - TEST: refactoring to pass planemo test using conda dependencies
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114
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115 **Version 1.0.0 - 10/02/2016**
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116
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117 - NEW: Create a summary of XCMS analysis
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118
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119
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120 ]]></help>
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121
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122
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123 <expand macro="citation" />
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124
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125 </tool>