Mercurial > repos > mmonsoor > camera_combinexsannos

comparison abims_CAMERA_combinexsAnnos.xml @ 4:87570e9b71f5 draft

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planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
author lecorguille
date Mon, 25 Apr 2016 11:07:23 -0400
parents 4ca5c7bbc6cf
children 198b035d4848
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3:4ca5c7bbc6cf 4:87570e9b71f5
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