Mercurial > repos > lecorguille > xcms_summary
comparison abims_xcms_summary.xml @ 32:de3b88417327 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
author | lecorguille |
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date | Tue, 03 Apr 2018 11:40:57 -0400 |
parents | 0b5521b78c92 |
children | 79fe34cedc56 |
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31:0b5521b78c92 | 32:de3b88417327 |
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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 <expand macro="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 </expand> | 12 </expand> |
12 | 13 |
13 <expand macro="stdio"/> | 14 <expand macro="stdio"/> |
14 | 15 |
15 <command><![CDATA[ | 16 <command><![CDATA[ |
16 $__tool_directory__/xcms_summary.r | 17 @COMMAND_RSCRIPT@/xcms_summary.r |
17 | 18 |
18 image '$image' | 19 image '$image' |
19 htmlOutput '$htmlOutput' | 20 htmlOutput '$htmlOutput' |
20 user_email $__user_email__ | 21 user_email $__user_email__ |
21 | 22 |
22 ]]></command> | 23 ]]></command> |
23 | 24 |
24 <inputs> | 25 <inputs> |
25 | 26 |
26 <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.)" /> |
27 | 28 |
28 </inputs> | 29 </inputs> |
29 | 30 |
30 <outputs> | 31 <outputs> |
31 <data name="htmlOutput" format="html" label="xcms summary html" /> | 32 <data name="htmlOutput" format="html" label="xcms summary html" /> |
32 </outputs> | 33 </outputs> |
33 | 34 |
34 <tests> | 35 <tests> |
35 <!--<test> | 36 <!--<test> |
36 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" /> | 37 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" ftype="rdata"/> |
37 <output name="htmlOutput" file="faahKO.xset.group.retcor.group.fillpeaks.summary.html" /> | 38 <output name="htmlOutput" file="faahKO.xset.group.retcor.group.fillpeaks.summary.html" /> |
38 </test>--> | 39 </test>--> |
39 <test> | 40 <test> |
40 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" /> | 41 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" ftype="rdata"/> |
41 <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" /> |
42 </test> | 43 </test> |
43 </tests> | 44 </tests> |
44 | 45 |
45 <help><![CDATA[ | 46 <help><![CDATA[ |
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.findchrompeaks 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 --------------------------------------------------- |