Mercurial > repos > mmonsoor > camera_combinexsannos
comparison abims_CAMERA_combinexsAnnos.xml @ 4:87570e9b71f5 draft
planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
author | lecorguille |
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date | Mon, 25 Apr 2016 11:07:23 -0400 |
parents | 4ca5c7bbc6cf |
children | 198b035d4848 |
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3:4ca5c7bbc6cf | 4:87570e9b71f5 |
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1 <tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.3"> | 1 <tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.4"> |
2 | 2 |
3 <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</description> | 3 <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</description> |
4 | 4 |
5 <requirements> | 5 <macros> |
6 <requirement type="package" version="3.1.2">R</requirement> | 6 <import>macros.xml</import> |
7 <requirement type="binary">Rscript</requirement> | 7 </macros> |
8 <requirement type="package" version="1.44.0">xcms</requirement> | 8 |
9 <requirement type="package" version="1.22.0">camera</requirement> | 9 <expand macro="requirements"/> |
10 <requirement type="package" version="2.2.0">camera_w4m_script</requirement> | 10 <expand macro="stdio"/> |
11 </requirements> | |
12 | |
13 <stdio> | |
14 <exit_code range="1:" level="fatal" /> | |
15 </stdio> | |
16 | 11 |
17 <command><![CDATA[ | 12 <command><![CDATA[ |
18 CAMERA.r | 13 @COMMAND_CAMERA_SCRIPT@ |
19 xfunction combinexsAnnos | 14 xfunction combinexsAnnos |
20 image_pos $image_pos | 15 image_pos $image_pos |
21 image_neg $image_neg | 16 image_neg $image_neg |
22 | 17 |
23 variableMetadataOutput $variableMetadata | 18 variableMetadataOutput $variableMetadata |
50 </outputs> | 45 </outputs> |
51 | 46 |
52 <tests> | 47 <tests> |
53 <test> | 48 <test> |
54 <!-- TODO: generer des vrais dataset pos et neg--> | 49 <!-- TODO: generer des vrais dataset pos et neg--> |
55 <param name="image_pos" value="xset.group.retcor.group.fillPeaks.annotate.positive.Rdata"/> | 50 <param name="image_pos" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.Rdata"/> |
56 <param name="image_neg" value="xset.group.retcor.group.fillPeaks.annotate.negative.Rdata"/> | 51 <param name="image_neg" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata"/> |
57 <param name="pos" value="TRUE"/> | 52 <param name="pos" value="TRUE"/> |
58 <param name="tol" value="2"/> | 53 <param name="tol" value="2"/> |
59 <param name="ruleset" value="1,1"/> | 54 <param name="ruleset" value="1,1"/> |
60 <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" /> | 55 <output name="variableMetadata" file="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" /> |
61 </test> | 56 </test> |
62 </tests> | 57 </tests> |
63 | 58 |
64 | 59 |
65 <help><![CDATA[ | 60 <help><![CDATA[ |
66 | 61 |
67 .. class:: infomark | 62 @HELP_AUTHORS@ |
68 | |
69 **Authors** Carsten Kuhl ckuhl@ipb-halle.de, Ralf Tautenhahn rtautenh@scripps.edu, Steffen Neumann sneumann@@ipb-halle.de | |
70 | |
71 .. class:: infomark | |
72 | |
73 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M] | |
74 | |
75 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. | |
76 | |
77 --------------------------------------------------- | |
78 | |
79 | |
80 | 63 |
81 ======================= | 64 ======================= |
82 Xcms.combinexsAnnos | 65 Xcms.combinexsAnnos |
83 ======================= | 66 ======================= |
84 | 67 |
207 --------------------------------------------------- | 190 --------------------------------------------------- |
208 | 191 |
209 Changelog/News | 192 Changelog/News |
210 -------------- | 193 -------------- |
211 | 194 |
195 **Version 2.0.4 - 21/04/2016** | |
196 | |
197 - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0 | |
198 | |
199 | |
212 **Version 2.0.3 - 10/02/2016** | 200 **Version 2.0.3 - 10/02/2016** |
213 | 201 |
214 - BUGFIX: better management of errors. Datasets remained green although the process failed | 202 - BUGFIX: better management of errors. Datasets remained green although the process failed |
215 | 203 |
216 - UPDATE: refactoring of internal management of inputs/outputs | 204 - UPDATE: refactoring of internal management of inputs/outputs |
228 - NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode | 216 - NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode |
229 | 217 |
230 | 218 |
231 ]]></help> | 219 ]]></help> |
232 | 220 |
233 <citations> | 221 <expand macro="citation" /> |
234 <citation type="doi"> 10.1021/ac202450g</citation> | |
235 <citation type="doi">10.1093/bioinformatics/btu813</citation> | |
236 </citations> | |
237 | 222 |
238 | 223 |
239 </tool> | 224 </tool> |
240 | 225 |
241 | 226 |