Mercurial > repos > lecorguille > xcms_fillpeaks

comparison abims_xcms_fillPeaks.xml @ 1:107a3de94c05 draft

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author lecorguille
date Fri, 08 Jan 2016 09:53:56 -0500
parents 30b01bcefda4
children 0df708800853
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0:30b01bcefda4 1:107a3de94c05
1 <tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.2"> 1 <tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.4">
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>
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 &amp;&amp; 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 </help> 205 ]]></help>
176 206
177 <citations> 207 <citations>
178 <citation type="doi">10.1021/ac051437y</citation> 208 <citation type="doi">10.1021/ac051437y</citation>
179 <citation type="doi">10.1093/bioinformatics/btu813</citation> 209 <citation type="doi">10.1093/bioinformatics/btu813</citation>
180 </citations> 210 </citations>