Mercurial > repos > lecorguille > xcms_summary

comparison abims_xcms_summary.xml @ 6:ca7c9a6da2c6 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
author lecorguille
date Fri, 08 Apr 2016 10:40:12 -0400
parents df7b3b846cb6
children ed8d80fc927c
comparison
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5:df7b3b846cb6 6:ca7c9a6da2c6
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
33 </outputs> 34 </outputs>
34 35
35 <tests> 36 <tests>
36 <test> 37 <test>
37 <param name="image" value="fillpeaks.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>