Mercurial > repos > lecorguille > xcms_xcmsset

comparison abims_xcms_xcmsSet.xml @ 31:eb15a3841da4 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40"
author workflow4metabolomics
date Tue, 28 Apr 2020 09:35:10 -0400
parents 14b1c52fae62
children b02d1992a43a
comparison
equal deleted inserted replaced
30:14b1c52fae62 31:eb15a3841da4
1 <tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@TOOL_VERSION@+galaxy1">
2 <description>Chromatographic peak detection</description> 2 <description>Chromatographic peak detection</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <import>macros_xcms.xml</import> 6 <import>macros_xcms.xml</import>
28 28
29 method $methods.method 29 method $methods.method
30 30
31 #if $methods.method == "CentWave": 31 #if $methods.method == "CentWave":
32 @COMMAND_CENTWAVE@ 32 @COMMAND_CENTWAVE@
33 peaklist $methods.CentWaveAdv.peaklist
33 ## List of regions-of-interest (ROI) 34 ## List of regions-of-interest (ROI)
34 #set $sectionROI = $methods.CentWaveAdv.CentWaveAdvROI 35 #set $sectionROI = $methods.CentWaveAdv.CentWaveAdvROI
35 @COMMAND_CENTWAVEADVROI@ 36 @COMMAND_CENTWAVEADVROI@
36 #elif $methods.method == "CentWavePredIso": 37 #elif $methods.method == "CentWavePredIso":
37 @COMMAND_CENTWAVE@ 38 @COMMAND_CENTWAVE@
59 #end if 60 #end if
60 max $methods.MatchedFilterAdv.max 61 max $methods.MatchedFilterAdv.max
61 snthresh $methods.MatchedFilterAdv.snthresh 62 snthresh $methods.MatchedFilterAdv.snthresh
62 steps $methods.MatchedFilterAdv.steps 63 steps $methods.MatchedFilterAdv.steps
63 mzdiff $methods.MatchedFilterAdv.mzdiff 64 mzdiff $methods.MatchedFilterAdv.mzdiff
65 peaklist $methods.MatchedFilterAdv.peaklist
64 #elif $methods.method == "MSW": 66 #elif $methods.method == "MSW":
65 snthresh $methods.snthresh 67 snthresh $methods.snthresh
66 verboseColumns $methods.verboseColumns 68 verboseColumns $methods.verboseColumns
67 scales "c($methods.scales)" 69 scales "c($methods.scales)"
68 nearbyPeak $methods.nearbyPeak 70 nearbyPeak $methods.nearbyPeak
101 <!-- CentWave --> 103 <!-- CentWave -->
102 <when value="CentWave"> 104 <when value="CentWave">
103 <expand macro="input_centwave"/> 105 <expand macro="input_centwave"/>
104 <section name="CentWaveAdv" title="Advanced Options" expanded="False"> 106 <section name="CentWaveAdv" title="Advanced Options" expanded="False">
105 <expand macro="input_centwaveAdv"/> 107 <expand macro="input_centwaveAdv"/>
108 <param argument="peaklist" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Get a list of found chromatographic peaks" help="Generates a tabular file with all the chromatographic peaks obtained." />
106 <section name="CentWaveAdvROI" title="List of regions-of-interest (ROI)" expanded="False"> 109 <section name="CentWaveAdvROI" title="List of regions-of-interest (ROI)" expanded="False">
107 <expand macro="input_centwaveAdvROI" optional="true"/> 110 <expand macro="input_centwaveAdvROI" optional="true"/>
108 </section> 111 </section>
109 </section> 112 </section>
110 </when> 113 </when>
132 <param argument="sigma" type="float" value="" optional="true" label="Standard deviation (width) of matched filtration model peak" help="Leave it to empty to calculate it using fwhm by default at fwhm/2.3548" /> 135 <param argument="sigma" type="float" value="" optional="true" label="Standard deviation (width) of matched filtration model peak" help="Leave it to empty to calculate it using fwhm by default at fwhm/2.3548" />
133 <param argument="max" type="integer" value="5" label="Maximum number of peaks that are expected/will be identified per slice" /> 136 <param argument="max" type="integer" value="5" label="Maximum number of peaks that are expected/will be identified per slice" />
134 <param argument="snthresh" type="integer" value="10" label="Signal to Noise ratio cutoff" help="defining the signal to noise cutoff to be used in the chromatographic peak detection step" /> 137 <param argument="snthresh" type="integer" value="10" label="Signal to Noise ratio cutoff" help="defining the signal to noise cutoff to be used in the chromatographic peak detection step" />
135 <param argument="steps" type="integer" value="2" label="Number of bins to be merged before filtration" help="(i.e. the number of neighboring bins that will be joined to the slice in which filtration and peak detection will be performed)" /> 138 <param argument="steps" type="integer" value="2" label="Number of bins to be merged before filtration" help="(i.e. the number of neighboring bins that will be joined to the slice in which filtration and peak detection will be performed)" />
136 <param argument="mzdiff" type="float" value="0.6" label="Minimum difference in m/z for peaks with overlapping Retention Times" help="By default: 0.8-binSize*steps " /> 139 <param argument="mzdiff" type="float" value="0.6" label="Minimum difference in m/z for peaks with overlapping Retention Times" help="By default: 0.8-binSize*steps " />
140 <param argument="peaklist" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Get a list of found chromatographic peaks" help="Generates a tabular file with all the chromatographic peaks obtained." />
137 <!-- index --> 141 <!-- index -->
138 </section> 142 </section>
139 </when> 143 </when>
140 144
141 <!-- CentWaveWithPredIsoROIs --> 145 <!-- CentWaveWithPredIsoROIs -->
181 </inputs> 185 </inputs>
182 186
183 <outputs> 187 <outputs>
184 <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="${image.name.rsplit('.',1)[0]}.xset.RData" from_work_dir="xcmsSet.RData" /> 188 <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="${image.name.rsplit('.',1)[0]}.xset.RData" from_work_dir="xcmsSet.RData" />
185 <data name="log" format="txt" label="${image.name.rsplit('.',1)[0]}.xset.log.txt" from_work_dir="log.txt" /> 189 <data name="log" format="txt" label="${image.name.rsplit('.',1)[0]}.xset.log.txt" from_work_dir="log.txt" />
190 <data name="peaklist_out1" format="tabular" label="${image.name[:-6]}.chromPeak_table.tsv" from_work_dir="chromPeak_table.tsv" >
191 <filter>methods['method'] == 'CentWave' and (methods['CentWaveAdv']['peaklist'])</filter>
192 </data>
193 <data name="peaklist_out2" format="tabular" label="${image.name[:-6]}.chromPeak_table.tsv" from_work_dir="chromPeak_table.tsv" >
194 <filter>methods['method'] == 'MatchedFilter' and (methods['MatchedFilterAdv']['peaklist'])</filter>
195 </data>
186 </outputs> 196 </outputs>
187 197
188 <tests> 198 <tests>
189 199
190 <!--<test> 200 <!--<test>
490 Changelog/News 500 Changelog/News
491 -------------- 501 --------------
492 502
493 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS 503 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
494 504
505 **Version 3.6.1+galaxy1 - 22/04/2020**
506
507 - NEW: possibility to get a tabular file with all the chromatographic peaks obtained with the CentWave and MatchedFilter methods.
508
509
495 @HELP_XCMS_NEWVERSION_3610@ 510 @HELP_XCMS_NEWVERSION_3610@
496 511
497 **Version 3.4.4.1 - 30/04/2019** 512 **Version 3.4.4.1 - 30/04/2019**
498 513
499 - BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms. 514 - BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms.