Mercurial > repos > lecorguille > xcms_summary

annotate abims_xcms_summary.xml @ 46:18d050f7b9d4 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
author workflow4metabolomics
date Mon, 03 Feb 2025 14:42:34 +0000
parents 43122259be1f
children
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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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15 <required_files>
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16 <include path="xcms_summary.r" />
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17 <include path="lib.r" />
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18 </required_files>
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19 <expand macro="stdio"/>
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20
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21 <command><![CDATA[
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22 @COMMAND_RSCRIPT@xcms_summary.r
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24 image '$image'
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25 htmlOutput '$htmlOutput'
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26 user_email $__user_email__
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27
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28 ]]></command>
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29
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30 <inputs>
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31
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32 <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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33
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34 </inputs>
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35
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36 <outputs>
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37 <data name="htmlOutput" format="html" label="xcms summary html" />
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38 </outputs>
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40 <tests>
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41 <!--<test>
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42 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" ftype="rdata"/>
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43 <output name="htmlOutput" file="faahKO.xset.group.retcor.group.fillpeaks.summary.html" />
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44 </test>-->
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45 <test>
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46 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" ftype="rdata"/>
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47 <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" lines_diff="2"/>
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48 </test>
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49 </tests>
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50
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51 <help><![CDATA[
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53 @HELP_AUTHORS@
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54
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55 ====================
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56 xcms process history
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57 ====================
0
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58
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59 -----------
0
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60 Description
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61 -----------
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62
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63 This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools
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64
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65 -----------------
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66 Workflow position
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67 -----------------
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69 **Upstream tools**
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70
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71 ========================= =========================== ================================
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72 Name Output file Format
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73 ========================= =========================== ================================
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74 xcms.findChromPeaks xset.RData rdata.xcms.findchrompeaks
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75 ------------------------- --------------------------- --------------------------------
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76 xcms.groupChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group
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77 ------------------------- --------------------------- --------------------------------
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78 xcms.adjustRtime ``*``.adjustRtime.RData rdata.xcms.retcor
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79 ------------------------- --------------------------- --------------------------------
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80 xcms.fillChromPeaks ``*``.fillChromPeaks.RData rdata.xcms.fillpeaks
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81 ------------------------- --------------------------- --------------------------------
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82 CAMERA.annotate ``*``.annotate.*.RData rdata.camera.``*``
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83 ========================= =========================== ================================
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85
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86 .. image:: xcms_summary_workflow.png
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87
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88 @HELP_XCMS_MANUAL@
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89
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90 ---------------------------------------------------
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91
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92 Changelog/News
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93 --------------
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94
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95 @HELP_XCMS_NEWVERSION_31200@
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96
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97 **Version 3.6.1+galaxy2 - 23/09/2020**
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99 - BUGFIX: "Error: object 'sampleNamesList' not found" in case of .RData input from CAMERA
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100
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101 **Version 3.6.1+galaxy1 - 05/04/2020**
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103 - UPGRADE: upgrade the CAMERA version from 1.38.0 to 1.42.0
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105 - BUGFIX: "Error in chromPeaks(from)[, "is_filled"] : subscript out of bounds"
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106
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107 @HELP_XCMS_NEWVERSION_3610@
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a7db001bfdaf "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
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109 @HELP_XCMS_NEWVERSION_3440@
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1d2cc6c87acf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
lecorguille
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110
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3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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111 **Version 3.0.0.0 - 14/02/2018**
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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112
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0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
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113 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
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114
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12c802da5367 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e131bacd37bfaf2c4132fd214c81db9b8a9df513
lecorguille
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115 - IMPROVEMENT: the tool now shows all the parameters and not only those which were set.
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0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
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116
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3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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117
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8ad83969888b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
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118 **Version 1.0.4 - 13/02/2018**
8ad83969888b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
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119
8ad83969888b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
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120 - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0
8ad83969888b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
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121
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0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
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122
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a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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123 **Version 1.0.3 - 03/02/2017**
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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124
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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125 - IMPROVEMENT: xcms.summary can deal with merged individual data
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
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126
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0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
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127
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c575dc541049 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
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128 **Version 1.0.2 - 06/07/2016**
c575dc541049 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
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129
c575dc541049 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
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130 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
c575dc541049 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
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131
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0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
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132
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dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
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133 **Version 1.0.1 - 04/04/2016**
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
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134
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
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135 - TEST: refactoring to pass planemo test using conda dependencies
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
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136
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
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137
0
6260844b9a17 planemo upload
lecorguille
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138 **Version 1.0.0 - 10/02/2016**
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lecorguille
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139
6260844b9a17 planemo upload
lecorguille
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140 - NEW: Create a summary of XCMS analysis
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lecorguille
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141
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lecorguille
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142
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lecorguille
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143 ]]></help>
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144
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145
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dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
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146 <expand macro="citation" />
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147
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lecorguille
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148 </tool>