Mercurial > repos > mmonsoor > camera_combinexsannos

comparison abims_CAMERA_combinexsAnnos.xml @ 3:4ca5c7bbc6cf draft

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planemo upload
author lecorguille
date Mon, 22 Feb 2016 16:49:04 -0500
parents 0c730c636867
children 87570e9b71f5
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2:46e8eb12f47b 3:4ca5c7bbc6cf
1 <tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.1"> 1 <tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.3">
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 <requirements>
6 <requirement type="package" version="3.1.2">R</requirement> 6 <requirement type="package" version="3.1.2">R</requirement>
7 <requirement type="binary">Rscript</requirement> 7 <requirement type="binary">Rscript</requirement>
8 <requirement type="package" version="1.44.0">xcms</requirement> 8 <requirement type="package" version="1.44.0">xcms</requirement>
9 <requirement type="package" version="1.22.0">camera</requirement> 9 <requirement type="package" version="1.22.0">camera</requirement>
10 <requirement type="package" version="2.1">camera_w4m_script</requirement> 10 <requirement type="package" version="2.2.0">camera_w4m_script</requirement>
11 </requirements> 11 </requirements>
12 12
13 <stdio> 13 <stdio>
14 <exit_code range="1:" level="fatal" /> 14 <exit_code range="1:" level="fatal" />
15 </stdio> 15 </stdio>
16 16
17 <command> 17 <command><![CDATA[
18 CAMERA.r 18 CAMERA.r
19 xfunction combinexsAnnos image_pos $image_pos image_neg $image_neg 19 xfunction combinexsAnnos
20 pos $pos tol $tol ruleset $ruleset convert_param $convert_param keep_meta $keep_meta &amp;&amp; ( 20 image_pos $image_pos
21 mv variableMetadata.tsv $variableMetadata); 21 image_neg $image_neg
22 cat xset.log 22
23 </command> 23 variableMetadataOutput $variableMetadata
24
25 pos $pos tol $tol ruleset $ruleset convert_param $convert_param keep_meta $keep_meta
26
27 ]]></command>
24 28
25 <inputs> 29 <inputs>
26 <param name="image_pos" type="data" label="Positive RData ion mode" format="rdata.camera.positive,rdata" help="output file from CAMERA.annotate using a positive polarity mode" /> 30 <param name="image_pos" type="data" label="Positive RData ion mode" format="rdata.camera.positive,rdata" help="output file from CAMERA.annotate using a positive polarity mode" />
27 <param name="image_neg" type="data" label="Negative RData ion mode" format="rdata.camera.negative,rdata" help="output file from CAMERA.annotate using a positive negative mode" /> 31 <param name="image_neg" type="data" label="Negative RData ion mode" format="rdata.camera.negative,rdata" help="output file from CAMERA.annotate using a positive negative mode" />
28 32
56 <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" /> 60 <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" />
57 </test> 61 </test>
58 </tests> 62 </tests>
59 63
60 64
61 <help> 65 <help><![CDATA[
62 66
63 .. class:: infomark 67 .. class:: infomark
64 68
65 **Authors** Carsten Kuhl ckuhl@ipb-halle.de, Ralf Tautenhahn rtautenh@scripps.edu, Steffen Neumann sneumann@@ipb-halle.de 69 **Authors** Carsten Kuhl ckuhl@ipb-halle.de, Ralf Tautenhahn rtautenh@scripps.edu, Steffen Neumann sneumann@@ipb-halle.de
66 70
197 201
198 **Example of an xset.combinexsAnnos.variableMetadata.tsv output:** 202 **Example of an xset.combinexsAnnos.variableMetadata.tsv output:**
199 203
200 .. image:: combinexsannos_variableMetadata.png 204 .. image:: combinexsannos_variableMetadata.png
201 205
202 </help> 206
207 ---------------------------------------------------
208
209 Changelog/News
210 --------------
211
212 **Version 2.0.3 - 10/02/2016**
213
214 - BUGFIX: better management of errors. Datasets remained green although the process failed
215
216 - UPDATE: refactoring of internal management of inputs/outputs
217
218
219 **Version 2.0.1 - 07/06/2015**
220
221 - IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors.
222
223 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
224
225
226 **Version 2.0.0 - 09/06/2015**
227
228 - NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode
229
230
231 ]]></help>
203 232
204 <citations> 233 <citations>
205 <citation type="doi"> 10.1021/ac202450g</citation> 234 <citation type="doi"> 10.1021/ac202450g</citation>
206 <citation type="doi">10.1093/bioinformatics/btu813</citation> 235 <citation type="doi">10.1093/bioinformatics/btu813</citation>
207 </citations> 236 </citations>