Mercurial > repos > lecorguille > xcms_fillpeaks
comparison abims_xcms_fillPeaks.xml @ 3:5a54397dbc97 draft
planemo upload
author | lecorguille |
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date | Mon, 22 Feb 2016 16:40:19 -0500 |
parents | 5815e6e11f9b |
children | 2edfa5e1f719 |
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2:5815e6e11f9b | 3:5a54397dbc97 |
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1 <tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.2"> | 1 <tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.5"> |
2 | 2 |
3 <description>Integrate the signal in the region of that peak group not represented and create a new peak</description> | 3 <description>Integrate the signal in the region of that peak group not represented and create a new peak</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="2.1">xcms_w4m_script</requirement> | 9 <requirement type="package" version="2.2.0">xcms_w4m_script</requirement> |
10 </requirements> | 10 </requirements> |
11 | 11 |
12 <stdio> | 12 <stdio> |
13 <exit_code range="1:" level="fatal" /> | 13 <exit_code range="1:" level="fatal" /> |
14 </stdio> | 14 </stdio> |
15 | 15 |
16 <command> | 16 <command><![CDATA[ |
17 xcms.r xfunction fillPeaks image $image method $method && mv fillPeaks.RData $xsetRData; cat xset.log | 17 xcms.r |
18 </command> | 18 xfunction fillPeaks |
19 image $image | |
20 | |
21 xsetRdataOutput $xsetRData | |
22 | |
23 method $method | |
24 | |
25 ###if $zip_file: | |
26 ## zipfile $zip_file | |
27 ###end if | |
28 ; | |
29 return=\$?; | |
30 mv log.txt $log; | |
31 cat $log; | |
32 sh -c "exit \$return" | |
33 | |
34 ]]></command> | |
19 | 35 |
20 <inputs> | 36 <inputs> |
21 <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (group)" /> | 37 <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (group)" /> |
22 <param name="method" type="select" label="Filling method" help="[method] See the help section below"> | 38 <param name="method" type="select" label="Filling method" help="[method] See the help section below"> |
23 <option value="chrom" selected="true">chrom</option> | 39 <option value="chrom" selected="true">chrom</option> |
24 <option value="MSW" >MSW</option> | 40 <option value="MSW" >MSW</option> |
25 </param> | 41 </param> |
42 <!-- To pass planemo test --> | |
43 <!--<param name="zip_file" type="hidden_data" format="no_unzip.zip" label="Zip file" />--> | |
26 </inputs> | 44 </inputs> |
27 | 45 |
28 <outputs> | 46 <outputs> |
29 <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" /> | 47 <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" /> |
48 <data name="log" format="txt" label="xset.log.txt" hidden="true" /> | |
30 </outputs> | 49 </outputs> |
31 | 50 |
32 <tests> | 51 <tests> |
33 <test> | 52 <test> |
34 <param name="image" value="xset.group.retcor.group.RData"/> | 53 <param name="image" value="xset.group.retcor.group.RData"/> |
35 <param name="method" value="chrom"/> | 54 <param name="method" value="chrom"/> |
36 <output name="xsetRData" file="xset.group.retcor.group.fillPeaks.RData" /> | 55 <param name="zip_file" value="sacuri.zip"/> |
56 <!--<output name="xsetRData" file="xset.group.retcor.group.fillPeaks.RData" />--> | |
57 <output name="log"> | |
58 <assert_contents> | |
59 <has_text text="object with 9 samples" /> | |
60 <has_text text="Time range: 0.7-1139.9 seconds (0-19 minutes)" /> | |
61 <has_text text="Mass range: 50.0019-999.9863 m/z" /> | |
62 <has_text text="Peaks: 157780 (about 17531 per sample)" /> | |
63 <has_text text="Peak Groups: 6761" /> | |
64 <has_text text="Sample classes: bio, blank" /> | |
65 </assert_contents> | |
66 </output> | |
37 </test> | 67 </test> |
38 </tests> | 68 </tests> |
39 | 69 |
40 <help> | 70 <help><![CDATA[ |
41 | 71 |
42 | 72 |
43 .. class:: infomark | 73 .. class:: infomark |
44 | 74 |
45 **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu | 75 **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu |
170 ------------ | 200 ------------ |
171 | 201 |
172 | **xset.fillPeaks.RData: RData file** | 202 | **xset.fillPeaks.RData: RData file** |
173 | 203 |
174 | 204 |
175 | 205 --------------------------------------------------- |
176 | 206 |
177 </help> | 207 Changelog/News |
208 -------------- | |
209 | |
210 **Version 2.0.5 - 10/02/2016** | |
211 | |
212 - BUGFIX: better management of errors. Datasets remained green although the process failed | |
213 | |
214 - UPDATE: refactoring of internal management of inputs/outputs | |
215 | |
216 - UPDATE: refactoring to feed the new report tool | |
217 | |
218 | |
219 **Version 2.0.2 - 02/06/2015** | |
220 | |
221 - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) 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 ]]></help> | |
178 | 227 |
179 <citations> | 228 <citations> |
180 <citation type="doi">10.1021/ac051437y</citation> | 229 <citation type="doi">10.1021/ac051437y</citation> |
181 <citation type="doi">10.1093/bioinformatics/btu813</citation> | 230 <citation type="doi">10.1093/bioinformatics/btu813</citation> |
182 </citations> | 231 </citations> |