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comparison abims_xcms_summary.xml @ 15:97ca0321931b draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
author lecorguille
date Tue, 18 Sep 2018 16:14:05 -0400
parents 4c757d1ba7b4
children 46be2c523a7f
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14:4c757d1ba7b4 15:97ca0321931b
1 <tool id="abims_xcms_summary" name="xcms.summary" version="1.0.4"> 1 <tool id="abims_xcms_summary" name="xcms process history" version="@WRAPPER_VERSION@.0">
2 2
3 <description>Create a summary of XCMS analysis</description> 3 <description>Create a summary of XCMS analysis</description>
4 4
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 <import>macros_xcms.xml</import>
7 </macros> 8 </macros>
8 9
9 <requirements> 10 <expand macro="requirements">
10 <requirement type="package" version="1.32.0">bioconductor-camera</requirement> 11 <requirement type="package" version="1.32.0">bioconductor-camera</requirement>
11 <requirement type="package" version="1.1_4">r-batch</requirement> 12 </expand>
12 </requirements>
13 13
14 <expand macro="stdio"/> 14 <expand macro="stdio"/>
15 15
16 <command><![CDATA[ 16 <command><![CDATA[
17 $__tool_directory__/xcms_summary.r 17 @COMMAND_RSCRIPT@/xcms_summary.r
18 18
19 image '$image' 19 image '$image'
20 htmlOutput '$htmlOutput' 20 htmlOutput '$htmlOutput'
21 user_email $__user_email__ 21 user_email $__user_email__
22 22
23 ]]></command> 23 ]]></command>
24 24
25 <inputs> 25 <inputs>
26 26
27 <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.)" /> 27 <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.)" />
28 28
29 </inputs> 29 </inputs>
30 30
31 <outputs> 31 <outputs>
32 <data name="htmlOutput" format="html" label="xcms summary html" /> 32 <data name="htmlOutput" format="html" label="xcms summary html" />
33 </outputs> 33 </outputs>
34 34
35 <tests> 35 <tests>
36 <!--<test>
37 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" ftype="rdata"/>
38 <output name="htmlOutput" file="faahKO.xset.group.retcor.group.fillpeaks.summary.html" />
39 </test>-->
36 <test> 40 <test>
37 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" /> 41 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" ftype="rdata"/>
38 <output name="htmlOutput" file="faahKO.xset.group.retcor.group.fillpeaks.summary.html" />
39 </test>
40 <test>
41 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" />
42 <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" /> 42 <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" />
43 </test> 43 </test>
44 </tests> 44 </tests>
45 45
46 <help><![CDATA[ 46 <help><![CDATA[
47 47
48 @HELP_AUTHORS@ 48 @HELP_AUTHORS@
49 49
50 ============ 50 ====================
51 Xcms.summary 51 xcms process history
52 ============ 52 ====================
53 53
54 ----------- 54 -----------
55 Description 55 Description
56 ----------- 56 -----------
57 57
61 Workflow position 61 Workflow position
62 ----------------- 62 -----------------
63 63
64 **Upstream tools** 64 **Upstream tools**
65 65
66 ========================= ================= ===================== ========== 66 ========================= =========================== ================================
67 Name output file format parameter 67 Name Output file Format
68 ========================= ================= ===================== ========== 68 ========================= =========================== ================================
69 xcms.xcmsSet xset.RData rdata.xcms.raw RData file 69 xcms.findChromPeaks xset.RData rdata.xcms.findchrompeaks
70 ------------------------- ----------------- --------------------- ---------- 70 ------------------------- --------------------------- --------------------------------
71 xcms.group xset.RData rdata.xcms.group RData file 71 xcms.groupChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group
72 ------------------------- ----------------- --------------------- ---------- 72 ------------------------- --------------------------- --------------------------------
73 xcms.retcor xset.RData rdata.xcms.retcor RData file 73 xcms.adjustRtime ``*``.adjustRtime.RData rdata.xcms.retcor
74 ------------------------- ----------------- --------------------- ---------- 74 ------------------------- --------------------------- --------------------------------
75 xcms.fillpeaks xset.RData rdata.xcms.fillpeaks RData file 75 xcms.fillChromPeaks ``*``.fillChromPeaks.RData rdata.xcms.fillpeaks
76 ------------------------- ----------------- --------------------- ---------- 76 ------------------------- --------------------------- --------------------------------
77 CAMERA.annotate xset.RData rdata.camera.* RData file 77 CAMERA.annotate ``*``.annotate.*.RData rdata.camera.``*``
78 ========================= ================= ===================== ========== 78 ========================= =========================== ================================
79 79
80 80
81 .. image:: xcms_summary_workflow.png 81 .. image:: xcms_summary_workflow.png
82 82
83 --------------------------------------------------- 83 ---------------------------------------------------
84 84
85 Changelog/News 85 Changelog/News
86 -------------- 86 --------------
87 87
88 **Version 3.0.0.0 - 14/02/2018**
89
90 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods
91
92 - IMPROVEMENT: the tool now shows all the parameters and not only those which were set.
93
94
88 **Version 1.0.4 - 13/02/2018** 95 **Version 1.0.4 - 13/02/2018**
89 96
90 - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0 97 - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0
98
91 99
92 **Version 1.0.3 - 03/02/2017** 100 **Version 1.0.3 - 03/02/2017**
93 101
94 - IMPROVEMENT: xcms.summary can deal with merged individual data 102 - IMPROVEMENT: xcms.summary can deal with merged individual data
95 103
104
96 **Version 1.0.2 - 06/07/2016** 105 **Version 1.0.2 - 06/07/2016**
97 106
98 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 107 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
108
99 109
100 **Version 1.0.1 - 04/04/2016** 110 **Version 1.0.1 - 04/04/2016**
101 111
102 - TEST: refactoring to pass planemo test using conda dependencies 112 - TEST: refactoring to pass planemo test using conda dependencies
103 113