Mercurial > repos > lecorguille > xcms_summary

comparison abims_xcms_summary.xml @ 12:27e7da5f6848 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
author lecorguille
date Fri, 07 Apr 2017 07:37:23 -0400
parents cb599006715f
children 4c757d1ba7b4
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11:cb599006715f 12:27e7da5f6848
1 <tool id="abims_xcms_summary" name="xcms.summary" version="1.0.2"> 1 <tool id="abims_xcms_summary" name="xcms.summary" version="1.0.3">
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 </macros> 7 </macros>
8 8
9 <requirements> 9 <requirements>
10 <requirement type="package" version="1.26.0">bioconductor-camera</requirement> 10 <requirement type="package" version="1.26.0">bioconductor-camera</requirement>
11 <requirement type="package" version="1.1_4">r-batch</requirement> 11 <requirement type="package" version="1.1_4">r-batch</requirement>
12 </requirements> 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 $__tool_directory__/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.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.)" />
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> 36 <test>
37 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" /> 37 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" />
38 <output name="htmlOutput" file="summary.html" /> 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" />
39 </test> 43 </test>
40 </tests> 44 </tests>
41 45
42 <help><![CDATA[ 46 <help><![CDATA[
43 47
44 @HELP_AUTHORS@ 48 @HELP_AUTHORS@
45 49
46 ============ 50 ============
47 Xcms.summary 51 Xcms.summary
48 ============ 52 ============
49 53
50 ----------- 54 -----------
51 Description 55 Description
52 ----------- 56 -----------
53 57
54 This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools 58 This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools
55 59
60 -----------------
61 Workflow position
62 -----------------
63
64 **Upstream tools**
65
66 ========================= ================= ===================== ==========
67 Name output file format parameter
68 ========================= ================= ===================== ==========
69 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
70 ------------------------- ----------------- --------------------- ----------
71 xcms.group xset.RData rdata.xcms.group RData file
72 ------------------------- ----------------- --------------------- ----------
73 xcms.retcor xset.RData rdata.xcms.retcor RData file
74 ------------------------- ----------------- --------------------- ----------
75 xcms.fillpeaks xset.RData rdata.xcms.fillpeaks RData file
76 ------------------------- ----------------- --------------------- ----------
77 CAMERA.annotate xset.RData rdata.camera.* RData file
78 ========================= ================= ===================== ==========
79
80
81 .. image:: xcms_summary_workflow.png
56 82
57 --------------------------------------------------- 83 ---------------------------------------------------
58 84
59 Changelog/News 85 Changelog/News
60 -------------- 86 --------------
87
88 **Version 1.0.3 - 03/02/2017**
89
90 - IMPROVEMENT: xcms.summary can deal with merged individual data
61 91
62 **Version 1.0.2 - 06/07/2016** 92 **Version 1.0.2 - 06/07/2016**
63 93
64 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 94 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
65 95