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comparison abims_xcms_summary.xml @ 0:930478b22633 draft

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author lecorguille
date Mon, 22 Feb 2016 16:44:04 -0500
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1 <tool id="abims_xcms_summary" name="xcms.summary" version="1.0.0">
2
3 <description>Create a summary of XCMS analysis</description>
4
5 <requirements>
6 <requirement type="package" version="3.1.2">R</requirement>
7 <requirement type="binary">Rscript</requirement>
8 <requirement type="package" version="1.44.0">xcms</requirement>
9 <requirement type="package" version="1.22.0">camera</requirement>
10 </requirements>
11
12 <stdio>
13 <exit_code range="1:" level="fatal" />
14 </stdio>
15
16 <command interpreter="Rscript"><![CDATA[
17 xcms_summary.r
18
19 image $image
20 htmlOutput $htmlOutput
21 user_email $__user_email__
22
23 ]]></command>
24
25 <inputs>
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.)" />
28
29 </inputs>
30
31 <outputs>
32 <data name="htmlOutput" format="html" label="xcms summary html" />
33 </outputs>
34
35 <tests>
36 <test>
37 <param name="image" value="fillpeaks.RData" />
38 <output name="htmlOutput" file="summary.html" />
39 </test>
40 </tests>
41
42 <help><![CDATA[
43
44 .. class:: infomark
45
46 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff part of Workflow4Metabolomics.org [W4M]
47
48 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
49
50 ---------------------------------------------------
51
52 ============
53 Xcms.summary
54 ============
55
56 -----------
57 Description
58 -----------
59
60 This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools
61
62
63 ---------------------------------------------------
64
65 Changelog/News
66 --------------
67
68 **Version 1.0.0 - 10/02/2016**
69
70 - NEW: Create a summary of XCMS analysis
71
72
73 ]]></help>
74
75
76 <citations>
77 <citation type="doi">10.1093/bioinformatics/btu813</citation>
78 </citations>
79
80 </tool>