Mercurial > repos > lecorguille > xcms_summary
comparison abims_xcms_summary.xml @ 28:8ad83969888b draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
author | lecorguille |
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date | Tue, 13 Feb 2018 04:45:13 -0500 |
parents | 33694028a409 |
children | 3d4339594010 |
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27:33694028a409 | 28:8ad83969888b |
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1 <tool id="abims_xcms_summary" name="xcms.summary" version="1.0.3"> | 1 <tool id="abims_xcms_summary" name="xcms.summary" version="1.0.4"> |
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="1.32.0">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 |
49 | 49 |
50 ============ | 50 ============ |
51 Xcms.summary | 51 Xcms.summary |
52 ============ | 52 ============ |
53 | 53 |
54 ----------- | |
54 Description | 55 Description |
55 ----------- | 56 ----------- |
56 | 57 |
57 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 |
58 | 59 |
59 | 60 ----------------- |
60 Workflow position | 61 Workflow position |
61 ----------------- | 62 ----------------- |
62 | 63 |
63 **Upstream tools** | 64 **Upstream tools** |
64 | 65 |
65 +------------------------+------------------+----------------------+------------+ | 66 ========================= ================= ===================== ========== |
66 | Name | output file | format | parameter | | 67 Name output file format parameter |
67 +========================+==================+======================+============+ | 68 ========================= ================= ===================== ========== |
68 | xcms.xcmsSet | xset.RData | rdata.xcms.raw | RData file | | 69 xcms.xcmsSet xset.RData rdata.xcms.raw RData file |
69 +------------------------+------------------+----------------------+------------+ | 70 ------------------------- ----------------- --------------------- ---------- |
70 | xcms.group | xset.RData | rdata.xcms.group | RData file | | 71 xcms.group xset.RData rdata.xcms.group RData file |
71 +------------------------+------------------+----------------------+------------+ | 72 ------------------------- ----------------- --------------------- ---------- |
72 | xcms.retcor | xset.RData | rdata.xcms.retcor | RData file | | 73 xcms.retcor xset.RData rdata.xcms.retcor RData file |
73 +------------------------+------------------+----------------------+------------+ | 74 ------------------------- ----------------- --------------------- ---------- |
74 | xcms.fillpeaks | xset.RData | rdata.xcms.fillpeaks | RData file | | 75 xcms.fillpeaks xset.RData rdata.xcms.fillpeaks RData file |
75 +------------------------+------------------+----------------------+------------+ | 76 ------------------------- ----------------- --------------------- ---------- |
76 | CAMERA.annotate | xset.RData | rdata.camera.* | RData file | | 77 CAMERA.annotate xset.RData rdata.camera.* RData file |
77 +------------------------+------------------+----------------------+------------+ | 78 ========================= ================= ===================== ========== |
78 | 79 |
79 | 80 |
80 .. image:: xcms_summary_workflow.png | 81 .. image:: xcms_summary_workflow.png |
81 | 82 |
82 --------------------------------------------------- | 83 --------------------------------------------------- |
83 | 84 |
84 Changelog/News | 85 Changelog/News |
85 -------------- | 86 -------------- |
87 | |
88 **Version 1.0.4 - 13/02/2018** | |
89 | |
90 - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0 | |
86 | 91 |
87 **Version 1.0.3 - 03/02/2017** | 92 **Version 1.0.3 - 03/02/2017** |
88 | 93 |
89 - IMPROVEMENT: xcms.summary can deal with merged individual data | 94 - IMPROVEMENT: xcms.summary can deal with merged individual data |
90 | 95 |