Mercurial > repos > lecorguille > xcms_fillpeaks

comparison abims_xcms_fillPeaks.xml @ 20:02bb34af0921 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
author lecorguille
date Wed, 08 Feb 2017 06:36:24 -0500
parents 7b74ec867ad2
children a6938c381d4e
comparison
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19:7b74ec867ad2 20:02bb34af0921
1 <tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.1.0"> 1 <tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.1.1">
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>
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
23 dataMatrixOutput $dataMatrix
24 convertRTMinute $peaklist.convertRTMinute
25 numDigitsMZ $peaklist.numDigitsMZ
26 numDigitsRT $peaklist.numDigitsRT
27 intval $peaklist.intval
28 #end if
29 22
30 @COMMAND_FILE_LOAD@ 23 @COMMAND_FILE_LOAD@
31 24
32 @COMMAND_LOG_EXIT@ 25 @COMMAND_LOG_EXIT@
33 26
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"/>
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="file_load"/> 38 <expand macro="file_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"/>
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>
293 --------------------------------------------------- 270 ---------------------------------------------------
294 271
295 Changelog/News 272 Changelog/News
296 -------------- 273 --------------
297 274
275 **Version 2.1.1 - 07/02/2017**
276
277 - 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)
278
298 **Version 2.1.0 - 03/02/2017** 279 **Version 2.1.0 - 03/02/2017**
299 280
300 - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data 281 - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data
301 282
302 **Version 2.0.8 - 22/12/2016** 283 **Version 2.0.8 - 22/12/2016**
309 290
310 **Version 2.0.6 - 04/04/2016** 291 **Version 2.0.6 - 04/04/2016**
311 292
312 - TEST: refactoring to pass planemo test using conda dependencies 293 - TEST: refactoring to pass planemo test using conda dependencies
313 294
314
315 **Version 2.0.5 - 10/02/2016** 295 **Version 2.0.5 - 10/02/2016**
316 296
317 - BUGFIX: better management of errors. Datasets remained green although the process failed 297 - BUGFIX: better management of errors. Datasets remained green although the process failed
318 298
319 - UPDATE: refactoring of internal management of inputs/outputs 299 - UPDATE: refactoring of internal management of inputs/outputs