Mercurial > repos > lecorguille > xcms_summary

annotate abims_xcms_summary.xml @ 45:43122259be1f draft

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
author workflow4metabolomics
date Mon, 15 Jul 2024 15:56:21 +0000
parents 9df658383852
children 18d050f7b9d4
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1 <tool id="abims_xcms_summary" name="xcms process history" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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="@TOOL_VERSION@">bioconductor-xcms</requirement>
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12 <requirement type="package" version="1.46.0">bioconductor-camera</requirement>
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13 <requirement type="package" version="1.1_5">r-batch</requirement>
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14 </requirements>
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16 <expand macro="stdio"/>
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18 <command><![CDATA[
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19 @COMMAND_RSCRIPT@/xcms_summary.r
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21 image '$image'
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22 htmlOutput '$htmlOutput'
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23 user_email $__user_email__
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24
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25 ]]></command>
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26
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27 <inputs>
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29 <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
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31 </inputs>
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32
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33 <outputs>
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34 <data name="htmlOutput" format="html" label="xcms summary html" />
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35 </outputs>
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37 <tests>
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38 <!--<test>
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39 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" ftype="rdata"/>
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40 <output name="htmlOutput" file="faahKO.xset.group.retcor.group.fillpeaks.summary.html" />
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41 </test>-->
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42 <test>
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43 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" ftype="rdata"/>
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44 <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" lines_diff="2"/>
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45 </test>
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46 </tests>
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47
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48 <help><![CDATA[
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50 @HELP_AUTHORS@
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51
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52 ====================
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53 xcms process history
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54 ====================
0
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55
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56 -----------
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57 Description
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58 -----------
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59
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60 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 -----------------
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63 Workflow position
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64 -----------------
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66 **Upstream tools**
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67
35
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68 ========================= =========================== ================================
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69 Name Output file Format
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70 ========================= =========================== ================================
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71 xcms.findChromPeaks xset.RData rdata.xcms.findchrompeaks
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72 ------------------------- --------------------------- --------------------------------
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73 xcms.groupChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group
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74 ------------------------- --------------------------- --------------------------------
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75 xcms.adjustRtime ``*``.adjustRtime.RData rdata.xcms.retcor
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76 ------------------------- --------------------------- --------------------------------
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77 xcms.fillChromPeaks ``*``.fillChromPeaks.RData rdata.xcms.fillpeaks
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78 ------------------------- --------------------------- --------------------------------
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79 CAMERA.annotate ``*``.annotate.*.RData rdata.camera.``*``
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80 ========================= =========================== ================================
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82
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83 .. image:: xcms_summary_workflow.png
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84
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85 @HELP_XCMS_MANUAL@
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86
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87 ---------------------------------------------------
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88
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89 Changelog/News
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90 --------------
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91
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92 @HELP_XCMS_NEWVERSION_31200@
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93
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94 **Version 3.6.1+galaxy2 - 23/09/2020**
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96 - BUGFIX: "Error: object 'sampleNamesList' not found" in case of .RData input from CAMERA
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97
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98 **Version 3.6.1+galaxy1 - 05/04/2020**
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100 - UPGRADE: upgrade the CAMERA version from 1.38.0 to 1.42.0
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102 - BUGFIX: "Error in chromPeaks(from)[, "is_filled"] : subscript out of bounds"
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103
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104 @HELP_XCMS_NEWVERSION_3610@
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105
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106 @HELP_XCMS_NEWVERSION_3440@
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107
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108 **Version 3.0.0.0 - 14/02/2018**
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109
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110 - 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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111
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12c802da5367 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
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112 - IMPROVEMENT: the tool now shows all the parameters and not only those which were set.
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113
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3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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114
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115 **Version 1.0.4 - 13/02/2018**
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116
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117 - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0
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118
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119
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a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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120 **Version 1.0.3 - 03/02/2017**
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121
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122 - IMPROVEMENT: xcms.summary can deal with merged individual data
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123
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124
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125 **Version 1.0.2 - 06/07/2016**
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126
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127 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
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128
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129
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130 **Version 1.0.1 - 04/04/2016**
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131
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132 - TEST: refactoring to pass planemo test using conda dependencies
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133
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134
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135 **Version 1.0.0 - 10/02/2016**
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136
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137 - NEW: Create a summary of XCMS analysis
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138
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139
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140 ]]></help>
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141
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142
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143 <expand macro="citation" />
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144
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145 </tool>