Mercurial > repos > lecorguille > xcms_summary

annotate abims_xcms_summary.xml @ 40:00be6777edc5 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a5136bfc124956893f4f0c91808d1c0d78c4ea01
author lecorguille
date Mon, 29 Apr 2019 06:15:21 -0400
parents 1d2cc6c87acf
children a7db001bfdaf
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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 <requirements>
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11 <requirement type="package" version="1.38.1">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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17 <command><![CDATA[
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18 @COMMAND_RSCRIPT@/xcms_summary.r
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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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24 ]]></command>
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26 <inputs>
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28 <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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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" ftype="rdata"/>
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39 <output name="htmlOutput" file="faahKO.xset.group.retcor.group.fillpeaks.summary.html" />
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40 </test>-->
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41 <test>
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42 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" ftype="rdata"/>
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43 <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" />
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44 </test>
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45 </tests>
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47 <help><![CDATA[
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49 @HELP_AUTHORS@
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51 ====================
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52 xcms process history
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53 ====================
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55 -----------
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56 Description
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57 -----------
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58
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59 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 Workflow position
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63 -----------------
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65 **Upstream tools**
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66
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67 ========================= =========================== ================================
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68 Name Output file Format
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69 ========================= =========================== ================================
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70 xcms.findChromPeaks xset.RData rdata.xcms.findchrompeaks
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71 ------------------------- --------------------------- --------------------------------
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72 xcms.groupChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group
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73 ------------------------- --------------------------- --------------------------------
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74 xcms.adjustRtime ``*``.adjustRtime.RData rdata.xcms.retcor
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75 ------------------------- --------------------------- --------------------------------
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76 xcms.fillChromPeaks ``*``.fillChromPeaks.RData rdata.xcms.fillpeaks
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77 ------------------------- --------------------------- --------------------------------
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78 CAMERA.annotate ``*``.annotate.*.RData rdata.camera.``*``
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79 ========================= =========================== ================================
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81
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82 .. image:: xcms_summary_workflow.png
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84 ---------------------------------------------------
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85
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86 Changelog/News
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87 --------------
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88
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89 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
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91 **Version 3.4.4.0 - 08/02/2019**
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93 - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_)
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95 **Version 3.0.0.0 - 14/02/2018**
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96
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97 - 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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99 - IMPROVEMENT: the tool now shows all the parameters and not only those which were set.
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102 **Version 1.0.4 - 13/02/2018**
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104 - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0
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105
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107 **Version 1.0.3 - 03/02/2017**
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109 - IMPROVEMENT: xcms.summary can deal with merged individual data
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110
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111
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112 **Version 1.0.2 - 06/07/2016**
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113
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114 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
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115
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116
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117 **Version 1.0.1 - 04/04/2016**
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118
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119 - TEST: refactoring to pass planemo test using conda dependencies
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120
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121
0
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122 **Version 1.0.0 - 10/02/2016**
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123
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124 - NEW: Create a summary of XCMS analysis
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125
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126
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127 ]]></help>
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128
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129
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130 <expand macro="citation" />
0
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131
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132 </tool>