Mercurial > repos > lecorguille > xcms_summary

annotate abims_xcms_summary.xml @ 20:d743af7feaad draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
author lecorguille
date Wed, 08 Feb 2017 06:36:43 -0500
parents a2908411620e
children abb66f65f1af
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
17
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
1 <tool id="abims_xcms_summary" name="xcms.summary" version="1.0.3">
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
2
0
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
3 <description>Create a summary of XCMS analysis</description>
9
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 8
diff changeset
4
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 8
diff changeset
5 <macros>
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 8
diff changeset
6 <import>macros.xml</import>
17
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
7 </macros>
9
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 8
diff changeset
8
0
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
9 <requirements>
16
339738598d55 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 15
diff changeset
10 <requirement type="package" version="1.26.0">bioconductor-camera</requirement>
9
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 8
diff changeset
11 <requirement type="package" version="1.1_4">r-batch</requirement>
0
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
12 </requirements>
17
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
13
9
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 8
diff changeset
14 <expand macro="stdio"/>
17
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
15
9
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 8
diff changeset
16 <command><![CDATA[
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 8
diff changeset
17 $__tool_directory__/xcms_summary.r
0
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
18
17
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
19 image $image
0
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
20 htmlOutput $htmlOutput
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
21 user_email $__user_email__
17
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
22
0
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
23 ]]></command>
17
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
24
0
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
25 <inputs>
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
26
9
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 8
diff changeset
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.)" />
0
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
28
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
29 </inputs>
17
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
30
0
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
31 <outputs>
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
32 <data name="htmlOutput" format="html" label="xcms summary html" />
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
33 </outputs>
17
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
34
0
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
35 <tests>
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
36 <test>
11
b302779347de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 9
diff changeset
37 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" />
17
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
38 <output name="htmlOutput" file="faahKO.xset.group.retcor.group.fillpeaks.summary.html" />
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
39 </test>
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
40 <test>
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
41 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" />
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
42 <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" />
0
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
43 </test>
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
44 </tests>
17
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
45
0
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
46 <help><![CDATA[
17
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
47
9
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 8
diff changeset
48 @HELP_AUTHORS@
0
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
49
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
50 ============
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
51 Xcms.summary
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
52 ============
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
53
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
54 -----------
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
55 Description
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
56 -----------
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
57
17
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
58 This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools
0
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
59
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
60
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
61 ---------------------------------------------------
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
62
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
63 Changelog/News
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
64 --------------
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
65
17
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
66 **Version 1.0.3 - 03/02/2017**
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
67
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
68 - IMPROVEMENT: xcms.summary can deal with merged individual data
a2908411620e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
69
14
c575dc541049 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 11
diff changeset
70 **Version 1.0.2 - 06/07/2016**
c575dc541049 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 11
diff changeset
71
c575dc541049 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 11
diff changeset
72 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
c575dc541049 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 11
diff changeset
73
9
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 8
diff changeset
74 **Version 1.0.1 - 04/04/2016**
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 8
diff changeset
75
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 8
diff changeset
76 - TEST: refactoring to pass planemo test using conda dependencies
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 8
diff changeset
77
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 8
diff changeset
78
0
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
79 **Version 1.0.0 - 10/02/2016**
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
80
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
81 - NEW: Create a summary of XCMS analysis
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
82
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
83
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
84 ]]></help>
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
85
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
86
9
dc6b3773f8de planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 1bf8810447bdd1268f67bfb64ead95ce82d8d85c
lecorguille
parents: 8
diff changeset
87 <expand macro="citation" />
0
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
88
6260844b9a17 planemo upload
lecorguille
parents:
diff changeset
89 </tool>