Mercurial > repos > lecorguille > xcms_summary
comparison abims_xcms_summary.xml @ 9:dc6b3773f8de draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
author | lecorguille |
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date | Fri, 08 Apr 2016 06:18:24 -0400 |
parents | 78fb71c535d0 |
children | b302779347de |
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8:78fb71c535d0 | 9:dc6b3773f8de |
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1 <tool id="abims_xcms_summary" name="xcms.summary" version="1.0.0"> | 1 <tool id="abims_xcms_summary" name="xcms.summary" version="1.0.1"> |
2 | 2 |
3 <description>Create a summary of XCMS analysis</description> | 3 <description>Create a summary of XCMS analysis</description> |
4 | 4 |
5 <macros> | |
6 <import>macros.xml</import> | |
7 </macros> | |
8 | |
5 <requirements> | 9 <requirements> |
6 <requirement type="package" version="3.1.2">R</requirement> | 10 <requirement type="package" version="3.1.2">R</requirement> |
7 <requirement type="binary">Rscript</requirement> | 11 <requirement type="package" version="1.22.0">bioconductor-camera</requirement> |
8 <requirement type="package" version="1.44.0">xcms</requirement> | 12 <requirement type="package" version="1.1_4">r-batch</requirement> |
9 <requirement type="package" version="1.22.0">camera</requirement> | |
10 </requirements> | 13 </requirements> |
11 | 14 |
12 <stdio> | 15 <expand macro="stdio"/> |
13 <exit_code range="1:" level="fatal" /> | |
14 </stdio> | |
15 | 16 |
16 <command interpreter="Rscript"><![CDATA[ | 17 <command><![CDATA[ |
17 xcms_summary.r | 18 $__tool_directory__/xcms_summary.r |
18 | 19 |
19 image $image | 20 image $image |
20 htmlOutput $htmlOutput | 21 htmlOutput $htmlOutput |
21 user_email $__user_email__ | 22 user_email $__user_email__ |
22 | 23 |
23 ]]></command> | 24 ]]></command> |
24 | 25 |
25 <inputs> | 26 <inputs> |
26 | 27 |
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,RData" label="xset RData file" help="output file from another function xcms (xcmsSet, group, retcor, fillpeaks etc.)" /> | 28 <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 |
29 </inputs> | 30 </inputs> |
30 | 31 |
31 <outputs> | 32 <outputs> |
32 <data name="htmlOutput" format="html" label="xcms summary html" /> | 33 <data name="htmlOutput" format="html" label="xcms summary html" /> |
33 </outputs> | 34 </outputs> |
34 | 35 |
35 <tests> | 36 <tests> |
36 <test> | 37 <test> |
37 <param name="image" value="fillpeaks.RData" ftype="RData" /> | 38 <param name="image" value="fillpeaks.RData" /> |
38 <output name="htmlOutput" file="summary.html" ftype="html" /> | 39 <output name="htmlOutput" file="summary.html" /> |
39 </test> | 40 </test> |
40 </tests> | 41 </tests> |
41 | 42 |
42 <help><![CDATA[ | 43 <help><![CDATA[ |
43 | 44 |
44 .. class:: infomark | 45 @HELP_AUTHORS@ |
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 | 46 |
52 ============ | 47 ============ |
53 Xcms.summary | 48 Xcms.summary |
54 ============ | 49 ============ |
55 | 50 |
63 --------------------------------------------------- | 58 --------------------------------------------------- |
64 | 59 |
65 Changelog/News | 60 Changelog/News |
66 -------------- | 61 -------------- |
67 | 62 |
63 **Version 1.0.1 - 04/04/2016** | |
64 | |
65 - TEST: refactoring to pass planemo test using conda dependencies | |
66 | |
67 | |
68 **Version 1.0.0 - 10/02/2016** | 68 **Version 1.0.0 - 10/02/2016** |
69 | 69 |
70 - NEW: Create a summary of XCMS analysis | 70 - NEW: Create a summary of XCMS analysis |
71 | 71 |
72 | 72 |
73 ]]></help> | 73 ]]></help> |
74 | 74 |
75 | 75 |
76 <citations> | 76 <expand macro="citation" /> |
77 <citation type="doi">10.1093/bioinformatics/btu813</citation> | |
78 </citations> | |
79 | 77 |
80 </tool> | 78 </tool> |