Mercurial > repos > lecorguille > xcms_summary

annotate abims_xcms_summary.xml @ 31:0b5521b78c92 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
author lecorguille
date Thu, 08 Mar 2018 05:55:26 -0500
parents 3d4339594010
children de3b88417327
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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 </macros>
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9 <expand macro="requirements">
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10 <requirement type="package" version="1.32.0">bioconductor-camera</requirement>
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11 </expand>
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13 <expand macro="stdio"/>
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15 <command><![CDATA[
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16 $__tool_directory__/xcms_summary.r
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18 image '$image'
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19 htmlOutput '$htmlOutput'
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20 user_email $__user_email__
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22 ]]></command>
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24 <inputs>
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26 <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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28 </inputs>
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30 <outputs>
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31 <data name="htmlOutput" format="html" label="xcms summary html" />
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32 </outputs>
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34 <tests>
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35 <!--<test>
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36 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" />
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37 <output name="htmlOutput" file="faahKO.xset.group.retcor.group.fillpeaks.summary.html" />
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38 </test>-->
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39 <test>
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40 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" />
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41 <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" />
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42 </test>
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43 </tests>
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44
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45 <help><![CDATA[
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47 @HELP_AUTHORS@
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49 ====================
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50 xcms process history
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51 ====================
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53 -----------
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54 Description
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55 -----------
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56
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57 This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools
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59 -----------------
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60 Workflow position
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61 -----------------
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63 **Upstream tools**
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64
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65 ========================= ================= ===================== ==========
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66 Name output file format parameter
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67 ========================= ================= ===================== ==========
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68 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
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69 ------------------------- ----------------- --------------------- ----------
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70 xcms.group xset.RData rdata.xcms.group RData file
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71 ------------------------- ----------------- --------------------- ----------
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72 xcms.retcor xset.RData rdata.xcms.retcor RData file
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73 ------------------------- ----------------- --------------------- ----------
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74 xcms.fillpeaks xset.RData rdata.xcms.fillpeaks RData file
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75 ------------------------- ----------------- --------------------- ----------
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76 CAMERA.annotate xset.RData rdata.camera.* RData file
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77 ========================= ================= ===================== ==========
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80 .. image:: xcms_summary_workflow.png
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82 ---------------------------------------------------
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83
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84 Changelog/News
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85 --------------
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86
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87 **Version 3.0.0.0 - 14/02/2018**
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88
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89 - 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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91 - IMPROVEMENT: the tool now shows all the parameters and not only those which were setted.
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94 **Version 1.0.4 - 13/02/2018**
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96 - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0
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99 **Version 1.0.3 - 03/02/2017**
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101 - IMPROVEMENT: xcms.summary can deal with merged individual data
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104 **Version 1.0.2 - 06/07/2016**
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106 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
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108
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109 **Version 1.0.1 - 04/04/2016**
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111 - TEST: refactoring to pass planemo test using conda dependencies
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113
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114 **Version 1.0.0 - 10/02/2016**
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115
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116 - NEW: Create a summary of XCMS analysis
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117
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118
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119 ]]></help>
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120
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121
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122 <expand macro="citation" />
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123
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124 </tool>