Mercurial > repos > lecorguille > xcms_fillpeaks
comparison abims_xcms_fillPeaks.xml @ 11:de0d85537ee3 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
author | lecorguille |
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date | Fri, 07 Apr 2017 07:37:05 -0400 |
parents | ee29f0a6e361 |
children | dcb9041cb9ea |
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10:6caa60dcc217 | 11:de0d85537ee3 |
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1 <tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.8"> | 1 <tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.1.0"> |
2 | 2 |
3 <description>Integrate a sample's signal in regions where peak groups are not represented to create new peaks in missing areas</description> | 3 <description>Integrate a sample's signal in regions where peak groups are not represented to create new peaks in missing areas</description> |
4 | 4 |
5 <macros> | 5 <macros> |
6 <import>macros.xml</import> | 6 <import>macros.xml</import> |
10 <expand macro="stdio"/> | 10 <expand macro="stdio"/> |
11 | 11 |
12 <command><![CDATA[ | 12 <command><![CDATA[ |
13 @COMMAND_XCMS_SCRIPT@ | 13 @COMMAND_XCMS_SCRIPT@ |
14 xfunction fillPeaks | 14 xfunction fillPeaks |
15 image $image | 15 image '$image' |
16 | 16 |
17 xsetRdataOutput $xsetRData | 17 xsetRdataOutput '$xsetRData' |
18 | 18 |
19 method $method | 19 method $method |
20 | 20 |
21 #if $peaklist.peaklistBool | 21 @COMMAND_PEAKLIST@ |
22 variableMetadataOutput $variableMetadata | 22 |
23 dataMatrixOutput $dataMatrix | 23 @COMMAND_FILE_LOAD@ |
24 convertRTMinute $peaklist.convertRTMinute | |
25 numDigitsMZ $peaklist.numDigitsMZ | |
26 numDigitsRT $peaklist.numDigitsRT | |
27 intval $peaklist.intval | |
28 #end if | |
29 | |
30 @COMMAND_ZIPFILE_LOAD@ | |
31 | 24 |
32 @COMMAND_LOG_EXIT@ | 25 @COMMAND_LOG_EXIT@ |
33 | 26 |
34 ]]></command> | 27 ]]></command> |
35 | 28 |
37 <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another xcms function (group)" /> | 30 <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another xcms function (group)" /> |
38 <param name="method" type="select" label="Filling method" help="[method] See the help section below"> | 31 <param name="method" type="select" label="Filling method" help="[method] See the help section below"> |
39 <option value="chrom" selected="true">chrom</option> | 32 <option value="chrom" selected="true">chrom</option> |
40 <option value="MSW" >MSW</option> | 33 <option value="MSW" >MSW</option> |
41 </param> | 34 </param> |
42 <conditional name="peaklist"> | 35 |
43 <param name="peaklistBool" type="boolean" label="Get a Peak List" /> | 36 <expand macro="input_peaklist"/> |
44 <when value="true"> | 37 |
45 <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/> | 38 <expand macro="input_file_load"/> |
46 <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" /> | |
47 <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" /> | |
48 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below"> | |
49 <option value="into" selected="true">into</option> | |
50 <option value="maxo">maxo</option> | |
51 <option value="intb">intb</option> | |
52 </param> | |
53 </when> | |
54 <when value="false" /> | |
55 </conditional> | |
56 <expand macro="zipfile_load"/> | |
57 | 39 |
58 </inputs> | 40 </inputs> |
59 | 41 |
60 <outputs> | 42 <outputs> |
61 <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" /> | 43 <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" /> |
62 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.fillPeaks.variableMetadata.tsv"> | 44 <expand macro="output_peaklist" function="fillpeaks" /> |
63 <filter>(peaklist['peaklistBool'])</filter> | |
64 </data> | |
65 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.fillPeaks.dataMatrix.tsv" > | |
66 <filter>(peaklist['peaklistBool'])</filter> | |
67 </data> | |
68 <data name="log" format="txt" label="xset.log.txt" hidden="true" /> | 45 <data name="log" format="txt" label="xset.log.txt" hidden="true" /> |
69 </outputs> | 46 </outputs> |
70 | 47 |
71 <tests> | 48 <tests> |
72 <!--<test> | 49 <!--<test> |
91 <param name="convertRTMinute" value="false" /> | 68 <param name="convertRTMinute" value="false" /> |
92 <param name="peaklistBool" value="true" /> | 69 <param name="peaklistBool" value="true" /> |
93 <param name="numDigitsMZ" value="4" /> | 70 <param name="numDigitsMZ" value="4" /> |
94 <param name="numDigitsRT" value="1" /> | 71 <param name="numDigitsRT" value="1" /> |
95 </conditional> | 72 </conditional> |
96 <param name="zipfile_load_conditional|zipfile_load_select" value="yes" /> | 73 <expand macro="test_file_load_zip"/> |
97 <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip" ftype="zip" /> | 74 <output name="log"> |
75 <assert_contents> | |
76 <has_text text="object with 4 samples" /> | |
77 <has_text text="Time range: 2506-4484 seconds (41.8-74.7 minutes)" /> | |
78 <has_text text="Mass range: 200.1-600 m/z" /> | |
79 <has_text text="Peaks: 32720 (about 8180 per sample)" /> | |
80 <has_text text="Peak Groups: 8157" /> | |
81 <has_text text="Sample classes: KO, WT" /> | |
82 </assert_contents> | |
83 </output> | |
84 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" /> | |
85 <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" /> | |
86 </test> | |
87 <test> | |
88 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.RData"/> | |
89 <param name="method" value="chrom"/> | |
90 <conditional name="peaklist"> | |
91 <param name="convertRTMinute" value="false" /> | |
92 <param name="peaklistBool" value="true" /> | |
93 <param name="numDigitsMZ" value="4" /> | |
94 <param name="numDigitsRT" value="1" /> | |
95 </conditional> | |
96 <expand macro="test_file_load_single"/> | |
98 <output name="log"> | 97 <output name="log"> |
99 <assert_contents> | 98 <assert_contents> |
100 <has_text text="object with 4 samples" /> | 99 <has_text text="object with 4 samples" /> |
101 <has_text text="Time range: 2506-4484 seconds (41.8-74.7 minutes)" /> | 100 <has_text text="Time range: 2506-4484 seconds (41.8-74.7 minutes)" /> |
102 <has_text text="Mass range: 200.1-600 m/z" /> | 101 <has_text text="Mass range: 200.1-600 m/z" /> |
267 --------------------------------------------------- | 266 --------------------------------------------------- |
268 | 267 |
269 Changelog/News | 268 Changelog/News |
270 -------------- | 269 -------------- |
271 | 270 |
271 **Version 2.1.0 - 07/02/2017** | |
272 | |
273 - IMPROVEMENT: change the management of the peaklist ids. The main ids remain the same as xcms generated. The export setiings now only add custom names in the variableMetadata tab (namecustom) | |
274 | |
275 - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data | |
276 | |
272 **Version 2.0.8 - 22/12/2016** | 277 **Version 2.0.8 - 22/12/2016** |
273 | 278 |
274 - IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate | 279 - IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate |
275 | 280 |
276 **Version 2.0.7 - 06/07/2016** | 281 **Version 2.0.7 - 06/07/2016** |
279 | 284 |
280 **Version 2.0.6 - 04/04/2016** | 285 **Version 2.0.6 - 04/04/2016** |
281 | 286 |
282 - TEST: refactoring to pass planemo test using conda dependencies | 287 - TEST: refactoring to pass planemo test using conda dependencies |
283 | 288 |
284 | |
285 **Version 2.0.5 - 10/02/2016** | 289 **Version 2.0.5 - 10/02/2016** |
286 | 290 |
287 - BUGFIX: better management of errors. Datasets remained green although the process failed | 291 - BUGFIX: better management of errors. Datasets remained green although the process failed |
288 | 292 |
289 - UPDATE: refactoring of internal management of inputs/outputs | 293 - UPDATE: refactoring of internal management of inputs/outputs |