Mercurial > repos > lecorguille > xcms_fillpeaks

comparison abims_xcms_fillPeaks.xml @ 19:7b74ec867ad2 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 717c02f887ce343ca55f862c8020aaf49f5581d8
author lecorguille
date Wed, 08 Feb 2017 05:27:41 -0500
parents 65dc5e8b53f7
children 02bb34af0921
comparison
equal deleted inserted replaced
18:65dc5e8b53f7 19:7b74ec867ad2
1 <tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.1.1"> 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>
16 16
17 xsetRdataOutput $xsetRData 17 xsetRdataOutput $xsetRData
18 18
19 method $method 19 method $method
20 20
21 @COMMAND_PEAKLIST@ 21 #if $peaklist.peaklistBool
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
22 29
23 @COMMAND_FILE_LOAD@ 30 @COMMAND_FILE_LOAD@
24 31
25 @COMMAND_LOG_EXIT@ 32 @COMMAND_LOG_EXIT@
26 33
30 <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another xcms function (group)" /> 37 <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another xcms function (group)" />
31 <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">
32 <option value="chrom" selected="true">chrom</option> 39 <option value="chrom" selected="true">chrom</option>
33 <option value="MSW" >MSW</option> 40 <option value="MSW" >MSW</option>
34 </param> 41 </param>
35 42 <conditional name="peaklist">
36 <expand macro="input_peaklist"/> 43 <param name="peaklistBool" type="boolean" label="Get a Peak List" />
37 44 <when value="true">
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>
38 <expand macro="file_load"/> 56 <expand macro="file_load"/>
39 57
40 </inputs> 58 </inputs>
41 59
42 <outputs> 60 <outputs>
43 <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" /> 61 <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" />
44 <expand macro="output_peaklist"/> 62 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.fillPeaks.variableMetadata.tsv">
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>
45 <data name="log" format="txt" label="xset.log.txt" hidden="true" /> 68 <data name="log" format="txt" label="xset.log.txt" hidden="true" />
46 </outputs> 69 </outputs>
47 70
48 <tests> 71 <tests>
49 <!--<test> 72 <!--<test>
270 --------------------------------------------------- 293 ---------------------------------------------------
271 294
272 Changelog/News 295 Changelog/News
273 -------------- 296 --------------
274 297
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
279 **Version 2.1.0 - 03/02/2017** 298 **Version 2.1.0 - 03/02/2017**
280 299
281 - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data 300 - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data
282 301
283 **Version 2.0.8 - 22/12/2016** 302 **Version 2.0.8 - 22/12/2016**
290 309
291 **Version 2.0.6 - 04/04/2016** 310 **Version 2.0.6 - 04/04/2016**
292 311
293 - TEST: refactoring to pass planemo test using conda dependencies 312 - TEST: refactoring to pass planemo test using conda dependencies
294 313
314
295 **Version 2.0.5 - 10/02/2016** 315 **Version 2.0.5 - 10/02/2016**
296 316
297 - BUGFIX: better management of errors. Datasets remained green although the process failed 317 - BUGFIX: better management of errors. Datasets remained green although the process failed
298 318
299 - UPDATE: refactoring of internal management of inputs/outputs 319 - UPDATE: refactoring of internal management of inputs/outputs