Mercurial > repos > lecorguille > xcms_summary
comparison abims_xcms_summary.xml @ 15:97ca0321931b draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
author | lecorguille |
---|---|
date | Tue, 18 Sep 2018 16:14:05 -0400 |
parents | 4c757d1ba7b4 |
children | 46be2c523a7f |
comparison
equal
deleted
inserted
replaced
14:4c757d1ba7b4 | 15:97ca0321931b |
---|---|
1 <tool id="abims_xcms_summary" name="xcms.summary" version="1.0.4"> | 1 <tool id="abims_xcms_summary" name="xcms process history" version="@WRAPPER_VERSION@.0"> |
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 <import>macros_xcms.xml</import> | |
7 </macros> | 8 </macros> |
8 | 9 |
9 <requirements> | 10 <expand macro="requirements"> |
10 <requirement type="package" version="1.32.0">bioconductor-camera</requirement> | 11 <requirement type="package" version="1.32.0">bioconductor-camera</requirement> |
11 <requirement type="package" version="1.1_4">r-batch</requirement> | 12 </expand> |
12 </requirements> | |
13 | 13 |
14 <expand macro="stdio"/> | 14 <expand macro="stdio"/> |
15 | 15 |
16 <command><![CDATA[ | 16 <command><![CDATA[ |
17 $__tool_directory__/xcms_summary.r | 17 @COMMAND_RSCRIPT@/xcms_summary.r |
18 | 18 |
19 image '$image' | 19 image '$image' |
20 htmlOutput '$htmlOutput' | 20 htmlOutput '$htmlOutput' |
21 user_email $__user_email__ | 21 user_email $__user_email__ |
22 | 22 |
23 ]]></command> | 23 ]]></command> |
24 | 24 |
25 <inputs> | 25 <inputs> |
26 | 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.)" /> | 27 <param name="image" type="data" format="rdata.xcms.findchrompeaks,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 | 28 |
29 </inputs> | 29 </inputs> |
30 | 30 |
31 <outputs> | 31 <outputs> |
32 <data name="htmlOutput" format="html" label="xcms summary html" /> | 32 <data name="htmlOutput" format="html" label="xcms summary html" /> |
33 </outputs> | 33 </outputs> |
34 | 34 |
35 <tests> | 35 <tests> |
36 <!--<test> | |
37 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" ftype="rdata"/> | |
38 <output name="htmlOutput" file="faahKO.xset.group.retcor.group.fillpeaks.summary.html" /> | |
39 </test>--> | |
36 <test> | 40 <test> |
37 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" /> | 41 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" ftype="rdata"/> |
38 <output name="htmlOutput" file="faahKO.xset.group.retcor.group.fillpeaks.summary.html" /> | |
39 </test> | |
40 <test> | |
41 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" /> | |
42 <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" /> | 42 <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" /> |
43 </test> | 43 </test> |
44 </tests> | 44 </tests> |
45 | 45 |
46 <help><![CDATA[ | 46 <help><![CDATA[ |
47 | 47 |
48 @HELP_AUTHORS@ | 48 @HELP_AUTHORS@ |
49 | 49 |
50 ============ | 50 ==================== |
51 Xcms.summary | 51 xcms process history |
52 ============ | 52 ==================== |
53 | 53 |
54 ----------- | 54 ----------- |
55 Description | 55 Description |
56 ----------- | 56 ----------- |
57 | 57 |
61 Workflow position | 61 Workflow position |
62 ----------------- | 62 ----------------- |
63 | 63 |
64 **Upstream tools** | 64 **Upstream tools** |
65 | 65 |
66 ========================= ================= ===================== ========== | 66 ========================= =========================== ================================ |
67 Name output file format parameter | 67 Name Output file Format |
68 ========================= ================= ===================== ========== | 68 ========================= =========================== ================================ |
69 xcms.xcmsSet xset.RData rdata.xcms.raw RData file | 69 xcms.findChromPeaks xset.RData rdata.xcms.findchrompeaks |
70 ------------------------- ----------------- --------------------- ---------- | 70 ------------------------- --------------------------- -------------------------------- |
71 xcms.group xset.RData rdata.xcms.group RData file | 71 xcms.groupChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group |
72 ------------------------- ----------------- --------------------- ---------- | 72 ------------------------- --------------------------- -------------------------------- |
73 xcms.retcor xset.RData rdata.xcms.retcor RData file | 73 xcms.adjustRtime ``*``.adjustRtime.RData rdata.xcms.retcor |
74 ------------------------- ----------------- --------------------- ---------- | 74 ------------------------- --------------------------- -------------------------------- |
75 xcms.fillpeaks xset.RData rdata.xcms.fillpeaks RData file | 75 xcms.fillChromPeaks ``*``.fillChromPeaks.RData rdata.xcms.fillpeaks |
76 ------------------------- ----------------- --------------------- ---------- | 76 ------------------------- --------------------------- -------------------------------- |
77 CAMERA.annotate xset.RData rdata.camera.* RData file | 77 CAMERA.annotate ``*``.annotate.*.RData rdata.camera.``*`` |
78 ========================= ================= ===================== ========== | 78 ========================= =========================== ================================ |
79 | 79 |
80 | 80 |
81 .. image:: xcms_summary_workflow.png | 81 .. image:: xcms_summary_workflow.png |
82 | 82 |
83 --------------------------------------------------- | 83 --------------------------------------------------- |
84 | 84 |
85 Changelog/News | 85 Changelog/News |
86 -------------- | 86 -------------- |
87 | 87 |
88 **Version 3.0.0.0 - 14/02/2018** | |
89 | |
90 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods | |
91 | |
92 - IMPROVEMENT: the tool now shows all the parameters and not only those which were set. | |
93 | |
94 | |
88 **Version 1.0.4 - 13/02/2018** | 95 **Version 1.0.4 - 13/02/2018** |
89 | 96 |
90 - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0 | 97 - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0 |
98 | |
91 | 99 |
92 **Version 1.0.3 - 03/02/2017** | 100 **Version 1.0.3 - 03/02/2017** |
93 | 101 |
94 - IMPROVEMENT: xcms.summary can deal with merged individual data | 102 - IMPROVEMENT: xcms.summary can deal with merged individual data |
95 | 103 |
104 | |
96 **Version 1.0.2 - 06/07/2016** | 105 **Version 1.0.2 - 06/07/2016** |
97 | 106 |
98 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 | 107 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 |
108 | |
99 | 109 |
100 **Version 1.0.1 - 04/04/2016** | 110 **Version 1.0.1 - 04/04/2016** |
101 | 111 |
102 - TEST: refactoring to pass planemo test using conda dependencies | 112 - TEST: refactoring to pass planemo test using conda dependencies |
103 | 113 |