Mercurial > repos > lecorguille > xcms_summary

annotate abims_xcms_summary.xml @ 26:db6549f27ad1 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8"
author workflow4metabolomics
date Tue, 12 May 2020 16:39:28 -0400
parents acc66e5c23d7
children bed23aa27b4b
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1 <tool id="abims_xcms_summary" name="xcms process history" version="@TOOL_VERSION@+galaxy1">
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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="1.40.0">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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25 ]]></command>
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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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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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36
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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" />
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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 ====================
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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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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
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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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83 .. image:: xcms_summary_workflow.png
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84
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85 ---------------------------------------------------
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86
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87 Changelog/News
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88 --------------
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89
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90 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
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91
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92 **Version 3.6.1+galaxy1 - 05/04/2020**
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94 - UPGRADE: upgrade the CAMERA version from 1.38.0 to 1.42.0
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96 - BUGFIX: "Error in chromPeaks(from)[, "is_filled"] : subscript out of bounds"
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97
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98 @HELP_XCMS_NEWVERSION_3610@
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99
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100 @HELP_XCMS_NEWVERSION_3440@
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101
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102 **Version 3.0.0.0 - 14/02/2018**
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104 - 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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106 - IMPROVEMENT: the tool now shows all the parameters and not only those which were set.
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108
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109 **Version 1.0.4 - 13/02/2018**
4c757d1ba7b4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
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110
4c757d1ba7b4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
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111 - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0
4c757d1ba7b4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
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112
15
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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113
12
27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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114 **Version 1.0.3 - 03/02/2017**
27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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115
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116 - IMPROVEMENT: xcms.summary can deal with merged individual data
27e7da5f6848 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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117
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97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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118
10
420f42a57916 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
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119 **Version 1.0.2 - 06/07/2016**
420f42a57916 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
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120
420f42a57916 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
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121 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
420f42a57916 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
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122
15
97ca0321931b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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123
6
ca7c9a6da2c6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
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124 **Version 1.0.1 - 04/04/2016**
ca7c9a6da2c6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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125
ca7c9a6da2c6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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126 - TEST: refactoring to pass planemo test using conda dependencies
ca7c9a6da2c6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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127
ca7c9a6da2c6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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128
0
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129 **Version 1.0.0 - 10/02/2016**
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130
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131 - NEW: Create a summary of XCMS analysis
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132
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133
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134 ]]></help>
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135
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136
6
ca7c9a6da2c6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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137 <expand macro="citation" />
0
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138
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139 </tool>