Mercurial > repos > lecorguille > xcms_summary
annotate abims_xcms_summary.xml @ 7:ed8d80fc927c draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
author | lecorguille |
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date | Mon, 25 Apr 2016 11:15:29 -0400 |
parents | ca7c9a6da2c6 |
children | 420f42a57916 |
rev | line source |
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ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
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1 <tool id="abims_xcms_summary" name="xcms.summary" version="1.0.1"> |
0 | 2 |
3 <description>Create a summary of XCMS analysis</description> | |
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ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
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4 |
ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
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5 <macros> |
ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
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6 <import>macros.xml</import> |
ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
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7 </macros> |
ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
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8 |
0 | 9 <requirements> |
10 <requirement type="package" version="3.1.2">R</requirement> | |
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ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
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11 <requirement type="package" version="1.22.0">bioconductor-camera</requirement> |
ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
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12 <requirement type="package" version="1.1_4">r-batch</requirement> |
0 | 13 </requirements> |
14 | |
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ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
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15 <expand macro="stdio"/> |
0 | 16 |
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ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
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17 <command><![CDATA[ |
ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
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18 $__tool_directory__/xcms_summary.r |
0 | 19 |
20 image $image | |
21 htmlOutput $htmlOutput | |
22 user_email $__user_email__ | |
23 | |
24 ]]></command> | |
25 | |
26 <inputs> | |
27 | |
28 <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.)" /> | |
29 | |
30 </inputs> | |
31 | |
32 <outputs> | |
33 <data name="htmlOutput" format="html" label="xcms summary html" /> | |
34 </outputs> | |
35 | |
36 <tests> | |
37 <test> | |
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ed8d80fc927c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents:
6
diff
changeset
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38 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" /> |
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ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
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39 <output name="htmlOutput" file="summary.html" /> |
0 | 40 </test> |
41 </tests> | |
42 | |
43 <help><![CDATA[ | |
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ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
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44 |
ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
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45 @HELP_AUTHORS@ |
0 | 46 |
47 ============ | |
48 Xcms.summary | |
49 ============ | |
50 | |
51 ----------- | |
52 Description | |
53 ----------- | |
54 | |
55 This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools | |
56 | |
57 | |
58 --------------------------------------------------- | |
59 | |
60 Changelog/News | |
61 -------------- | |
62 | |
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ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
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63 **Version 1.0.1 - 04/04/2016** |
ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
|
64 |
ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
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65 - TEST: refactoring to pass planemo test using conda dependencies |
ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
|
66 |
ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
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67 |
0 | 68 **Version 1.0.0 - 10/02/2016** |
69 | |
70 - NEW: Create a summary of XCMS analysis | |
71 | |
72 | |
73 ]]></help> | |
74 | |
75 | |
6
ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
|
76 <expand macro="citation" /> |
0 | 77 |
78 </tool> |