Mercurial > repos > lecorguille > xcms_fillpeaks
comparison abims_xcms_fillPeaks.xml @ 4:2edfa5e1f719 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
author | lecorguille |
---|---|
date | Fri, 08 Apr 2016 10:39:59 -0400 |
parents | 5a54397dbc97 |
children | cd351af95d14 |
comparison
equal
deleted
inserted
replaced
3:5a54397dbc97 | 4:2edfa5e1f719 |
---|---|
1 <tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.5"> | 1 <tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.6"> |
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 <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="2.2.0">xcms_w4m_script</requirement> | 9 <expand macro="requirements"/> |
10 </requirements> | 10 <expand macro="stdio"/> |
11 | |
12 <stdio> | |
13 <exit_code range="1:" level="fatal" /> | |
14 </stdio> | |
15 | 11 |
16 <command><![CDATA[ | 12 <command><![CDATA[ |
17 xcms.r | 13 @COMMAND_XCMS_SCRIPT@ |
18 xfunction fillPeaks | 14 xfunction fillPeaks |
19 image $image | 15 image $image |
20 | 16 |
21 xsetRdataOutput $xsetRData | 17 xsetRdataOutput $xsetRData |
22 | 18 |
23 method $method | 19 method $method |
24 | 20 |
25 ###if $zip_file: | 21 #if $zip_file: |
26 ## zipfile $zip_file | 22 zipfile $zip_file |
27 ###end if | 23 #end if |
28 ; | 24 @COMMAND_LOG_EXIT@ |
29 return=\$?; | |
30 mv log.txt $log; | |
31 cat $log; | |
32 sh -c "exit \$return" | |
33 | 25 |
34 ]]></command> | 26 ]]></command> |
35 | 27 |
36 <inputs> | 28 <inputs> |
37 <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (group)" /> | 29 <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (group)" /> |
38 <param name="method" type="select" label="Filling method" help="[method] See the help section below"> | 30 <param name="method" type="select" label="Filling method" help="[method] See the help section below"> |
39 <option value="chrom" selected="true">chrom</option> | 31 <option value="chrom" selected="true">chrom</option> |
40 <option value="MSW" >MSW</option> | 32 <option value="MSW" >MSW</option> |
41 </param> | 33 </param> |
42 <!-- To pass planemo test --> | 34 <!-- To pass planemo test --> |
43 <!--<param name="zip_file" type="hidden_data" format="no_unzip.zip" label="Zip file" />--> | 35 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." /> |
44 </inputs> | 36 </inputs> |
45 | 37 |
46 <outputs> | 38 <outputs> |
47 <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" /> | 39 <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" /> | 40 <data name="log" format="txt" label="xset.log.txt" hidden="true" /> |
50 | 42 |
51 <tests> | 43 <tests> |
52 <test> | 44 <test> |
53 <param name="image" value="xset.group.retcor.group.RData"/> | 45 <param name="image" value="xset.group.retcor.group.RData"/> |
54 <param name="method" value="chrom"/> | 46 <param name="method" value="chrom"/> |
55 <param name="zip_file" value="sacuri.zip"/> | 47 <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" /> |
56 <!--<output name="xsetRData" file="xset.group.retcor.group.fillPeaks.RData" />--> | |
57 <output name="log"> | 48 <output name="log"> |
58 <assert_contents> | 49 <assert_contents> |
59 <has_text text="object with 9 samples" /> | 50 <has_text text="object with 4 samples" /> |
60 <has_text text="Time range: 0.7-1139.9 seconds (0-19 minutes)" /> | 51 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" /> |
61 <has_text text="Mass range: 50.0019-999.9863 m/z" /> | 52 <has_text text="Mass range: 50.0021-999.9863 m/z" /> |
62 <has_text text="Peaks: 157780 (about 17531 per sample)" /> | 53 <has_text text="Peaks: 199718 (about 49930 per sample)" /> |
63 <has_text text="Peak Groups: 6761" /> | 54 <has_text text="Peak Groups: 48958" /> |
64 <has_text text="Sample classes: bio, blank" /> | 55 <has_text text="Sample classes: bio, blank" /> |
65 </assert_contents> | 56 </assert_contents> |
66 </output> | 57 </output> |
67 </test> | 58 </test> |
68 </tests> | 59 </tests> |
69 | 60 |
70 <help><![CDATA[ | 61 <help><![CDATA[ |
71 | |
72 | 62 |
73 .. class:: infomark | 63 @HELP_AUTHORS@ |
74 | |
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 | |
76 | |
77 .. class:: infomark | |
78 | |
79 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M] | |
80 | |
81 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. | |
82 | |
83 | |
84 --------------------------------------------------- | |
85 | 64 |
86 ============== | 65 ============== |
87 Xcms.fillPeaks | 66 Xcms.fillPeaks |
88 ============== | 67 ============== |
89 | 68 |
205 --------------------------------------------------- | 184 --------------------------------------------------- |
206 | 185 |
207 Changelog/News | 186 Changelog/News |
208 -------------- | 187 -------------- |
209 | 188 |
189 **Version 2.0.6 - 04/04/2016** | |
190 | |
191 - TEST: refactoring to pass planemo test using conda dependencies | |
192 | |
193 | |
210 **Version 2.0.5 - 10/02/2016** | 194 **Version 2.0.5 - 10/02/2016** |
211 | 195 |
212 - BUGFIX: better management of errors. Datasets remained green although the process failed | 196 - BUGFIX: better management of errors. Datasets remained green although the process failed |
213 | 197 |
214 - UPDATE: refactoring of internal management of inputs/outputs | 198 - UPDATE: refactoring of internal management of inputs/outputs |
223 - IMPROVEMENT: parameter labels have changed to facilitate their reading. | 207 - IMPROVEMENT: parameter labels have changed to facilitate their reading. |
224 | 208 |
225 | 209 |
226 ]]></help> | 210 ]]></help> |
227 | 211 |
228 <citations> | 212 |
229 <citation type="doi">10.1021/ac051437y</citation> | 213 <expand macro="citation" /> |
230 <citation type="doi">10.1093/bioinformatics/btu813</citation> | |
231 </citations> | |
232 | 214 |
233 | 215 |
234 </tool> | 216 </tool> |