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>