Mercurial > repos > lecorguille > xcms_xcmsset

annotate abims_xcms_xcmsSet.xml @ 18:517d4375db53 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty
author lecorguille
date Thu, 04 Oct 2018 10:34:58 -0400
parents ea974024a6c6
children 87df3692c68d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
1 <tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@WRAPPER_VERSION@.0">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
2 <description>Chromatographic peak detection</description>
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
3
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
4 <macros>
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
5 <import>macros.xml</import>
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
6 <import>macros_xcms.xml</import>
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
7 </macros>
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
8
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
9 <expand macro="requirements"/>
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
10 <expand macro="stdio"/>
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
11
5
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
12 <command><![CDATA[
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
13 @COMMAND_RSCRIPT@/xcms_xcmsSet.r
12
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
14
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
15 image '$image'
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
16
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
17 BPPARAM \${GALAXY_SLOTS:-1}
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
18
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
19 #if $filterSection.filterAcquisitionNum != "":
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
20 filterAcquisitionNum "c($filterSection.filterAcquisitionNum)"
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
21 #end if
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
22 #if $filterSection.filterRt != "":
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
23 filterRt "c($filterSection.filterRt)"
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
24 #end if
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
25 #if $filterSection.filterMz != "":
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
26 filterMz "c($filterSection.filterMz)"
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
27 #end if
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
28
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
29 method $methods.method
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
30
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
31 #if $methods.method == "CentWave":
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
32 @COMMAND_CENTWAVE@
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
33 ## List of regions-of-interest (ROI)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
34 #set $sectionROI = $methods.CentWaveAdv.CentWaveAdvROI
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
35 @COMMAND_CENTWAVEADVROI@
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
36 #elif $methods.method == "CentWavePredIso":
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
37 @COMMAND_CENTWAVE@
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
38 ## List of regions-of-interest (ROI)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
39 #set $sectionROI = $methods.CentWaveAdvROI
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
40 @COMMAND_CENTWAVEADVROI@
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
41 snthreshIsoROIs $sectionROI.snthreshIsoROIs
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
42 maxCharge $sectionROI.maxCharge
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
43 maxIso $sectionROI.maxIso
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
44 mzIntervalExtension $sectionROI.mzIntervalExtension
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
45 polarity $sectionROI.polarity
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
46 #elif $methods.method == "MatchedFilter":
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
47 fwhm $methods.fwhm
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
48 binSize $methods.binSize
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
49 ## Advanced
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
50 impute $methods.MatchedFilterAdv.impute_cond.impute
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
51 #if $methods.MatchedFilterAdv.impute_cond.impute == "linbase":
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
52 #if $methods.MatchedFilterAdv.impute_cond.baseValue != "":
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
53 baseValue $methods.MatchedFilterAdv.impute_cond.baseValue
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
54 #end if
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
55 distance $methods.MatchedFilterAdv.impute_cond.distance
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
56 #end if
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
57 #if $methods.MatchedFilterAdv.sigma != "":
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
58 sigma $methods.MatchedFilterAdv.sigma
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
59 #end if
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
60 max $methods.MatchedFilterAdv.max
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
61 snthresh $methods.MatchedFilterAdv.snthresh
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
62 steps $methods.MatchedFilterAdv.steps
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
63 mzdiff $methods.MatchedFilterAdv.mzdiff
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
64 #elif $methods.method == "MSW":
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
65 snthresh $methods.snthresh
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
66 verboseColumns $methods.verboseColumns
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
67 scales "c($methods.scales)"
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
68 nearbyPeak $methods.nearbyPeak
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
69 ampTh $methods.ampTh
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
70 #end if
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
71
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
72 @COMMAND_FILE_LOAD@
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
73
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
74 @COMMAND_LOG_EXIT@
5
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
75 ]]></command>
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
76
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
77 <inputs>
054e4681667c planemo upload
lecorguille
parents:
diff changeset
78
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
79 <param name="image" type="data" format="rdata.msnbase.raw,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from MSnbase readMSData" />
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
80
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
81 <section name="filterSection" title="Spectra Filters" expanded="False">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
82 <param argument="filterAcquisitionNum" type="text" value="" optional="true" label="Filter on Acquisition Numbers" help="min,max">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
83 <expand macro="input_validator_range_integer"/>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
84 </param>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
85 <param argument="filterRt" type="text" value="" optional="true" label="Filter on Retention Time" help="min,max">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
86 <expand macro="input_validator_range_integer"/>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
87 </param>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
88 <param argument="filterMz" type="text" value="" optional="true" label="Filter on Mz" help="min,max">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
89 <expand macro="input_validator_range_integer"/>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
90 </param>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
91 </section>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
92
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
93 <conditional name="methods">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
94 <param name="method" type="select" label="Extraction method for peaks detection" help="See the help section below">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
95 <option value="MatchedFilter" selected="true">MatchedFilter - peak detection in chromatographic space</option>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
96 <option value="CentWave">CentWave - chromatographic peak detection using the centWave method</option>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
97 <option value="CentWavePredIso">CentWaveWithPredIsoROIs - performs a two-step centWave-based chromatographic peak detection</option>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
98 <option value="MSW">MSW - single-spectrum non-chromatography MS data peak detection</option>
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
99 </param>
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
100
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
101 <!-- CentWave -->
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
102 <when value="CentWave">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
103 <expand macro="input_centwave"/>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
104 <section name="CentWaveAdv" title="Advanced Options" expanded="False">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
105 <expand macro="input_centwaveAdv"/>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
106 <section name="CentWaveAdvROI" title="List of regions-of-interest (ROI)" expanded="False">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
107 <expand macro="input_centwaveAdvROI" optional="true"/>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
108 </section>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
109 </section>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
110 </when>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
111
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
112 <!-- MatchedFilter -->
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
113 <when value="MatchedFilter">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
114 <param argument="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="Only used to calculate the actual sigma" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
115 <param argument="binSize" type="float" value="0.1" label="Step size to use for profile generation" help="The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size. (Previously step)" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
116 <section name="MatchedFilterAdv" title="Advanced Options" expanded="False">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
117 <conditional name="impute_cond">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
118 <param argument="impute" type="select" label="Method to be used for missing value imputation" help="(previously profmethod)">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
119 <option value="none">none - no linear interpolation</option>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
120 <option value="lin">lin - linear interpolation</option>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
121 <option value="linbase">linbase - linear interpolation within a certain bin-neighborhood</option>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
122 <option value="intlin">intlin - integral of the linearly interpolated data from plus to minus half the step size</option>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
123 </param>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
124 <when value="none" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
125 <when value="lin" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
126 <when value="linbase">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
127 <param argument="baseValue" type="float" value="" optional="true" label="The base value to which empty elements should be set" help="The default for the ‘baseValue’ is half of the smallest value in ‘x’ (‘NA’s being removed)." />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
128 <param argument="distance" type="integer" value="0" label="Number of non-empty neighboring element of an empty element that should be considered for linear interpolation." />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
129 </when>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
130 <when value="intlin" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
131 </conditional>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
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" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
133 <param argument="max" type="integer" value="5" label="Maximum number of peaks that are expected/will be identified per slice" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
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" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
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)" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
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 " />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
137 <!-- index -->
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
138 </section>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
139 </when>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
140
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
141 <!-- CentWaveWithPredIsoROIs -->
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
142 <when value="CentWavePredIso">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
143 <expand macro="input_centwave"/>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
144 <section name="CentWaveAdv" title="Advanced Options" expanded="False">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
145 <expand macro="input_centwaveAdv"/>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
146 </section>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
147 <section name="CentWaveAdvROI" title="List of regions-of-interest (ROI)" expanded="True">
17
ea974024a6c6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 8dfca81480bcbfb5b164ee736b2e2cad324ad8a1-dirty
lecorguille
parents: 15
diff changeset
148 <expand macro="input_centwaveAdvROI" optional="true" />
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
149 <param argument="snthreshIsoROIs" type="float" value="6.25" label="Signal to noise ratio cutoff" help="used in the second centWave run to identify peaks for predicted isotope ROIs." />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
150 <param argument="maxCharge" type="integer" value="3" label="Maximal isotope charge" help="Isotopes will be defined for charges ‘1:maxCharge’." />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
151 <param argument="maxIso" type="integer" value="5" label="Number of isotope peaks that should be predicted for each peak identified in the first centWave run" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
152 <param argument="mzIntervalExtension" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Is the mz range for the predicted isotope ROIs should be extended to increase detection of low intensity peaks" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
153 <param argument="polarity" type="select" label="Polarity of the data">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
154 <option value="unknown">unknown</option>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
155 <option value="positive">positive</option>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
156 <option value="negative">negative</option>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
157 </param>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
158 </section>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
159 </when>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
160
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
161 <!-- MSW -->
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
162 <when value="MSW">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
163 <!---@TODO <param argument="winSize_noise" type="integer" value="500" label="The local window size to estimate the noise level" help="[winSize.noise]" />-->
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
164 <param argument="snthresh" type="integer" value="3" label="Signal to Noise ratio cutoff" help="" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
165 <param argument="verboseColumns" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="verbose Columns" help="whether additional peak meta data columns should be returned" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
166 <param argument="scales" type="text" value="1,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,36,40,44,48,52,56,60,64" label="Scales of the Continuous Wavelet Transform (CWT)" help="Scales are linked to the width of the peaks that are to be detected." >
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
167 <expand macro="input_validator_list_integer"/>
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
168 </param>
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
169 <param argument="nearbyPeak" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Determine whether to include the nearby small peaks of major peaks" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
170 <!-- peakScaleRange -->
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
171 <param argument="ampTh" type="float" value="0.01" label="Minimum required relative amplitude of the peak" help="Ratio to the maximum of CWT coefficients" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
172 <!-- minNoiseLevel -->
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
173 <!-- ridgeLength -->
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
174 <!-- peakThr -->
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
175 <!-- tuneIn -->
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
176 <!---@TODO <param argument="SNR_method" type="text" value="data.mean" label="SNR (Signal to Noise Ratio) method" help="[SNR.method] Method to estimate noise level. Currently, only 95 percentage quantile is supported." />-->
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
177 </when>
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
178 </conditional>
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
179
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
180 <expand macro="input_file_load"/>
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
181 </inputs>
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
182
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
183 <outputs>
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
184 <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="${image.name.rsplit('.',1)[0]}.xset.RData" from_work_dir="xcmsSet.RData" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
185 <data name="log" format="txt" label="${image.name.rsplit('.',1)[0]}.xset.log.txt" from_work_dir="log.txt" />
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
186 </outputs>
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
187
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
188 <tests>
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
189
7
451ff602a957 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
190 <!--<test>
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
191 <param name="image" value="faahKO.raw.Rdata" ftype="rdata" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
192 <section name="filterSection">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
193 <param name="filterAcquisitionNum" value="100,5000" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
194 <param name="filterRt" value="3000,4000" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
195 <param name="filterMz" value="300,400" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
196 </section>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
197 <conditional name="methods">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
198 <param name="method" value="CentWave" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
199 <param name="ppm" value="25" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
200 <param name="peakwidth" value="20,50" />-->
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
201 <!-- DISABLE: just for testing the arguments
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
202 <section name="CentWaveAdv">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
203 <section name="CentWaveAdvROI">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
204 <param name="roiList" value="roiList.txt" ftype="tabular" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
205 </section>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
206 </section>-->
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
207 <!--</conditional>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
208 <expand macro="test_file_load_zip"/>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
209 <assert_stdout>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
210 <has_text text="ppm: 25" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
211 <has_text text="peakwidth: 20, 50" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
212 <has_text text="object with 4 samples" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
213 <has_text text="Time range: 3006.9-3978.7 seconds (50.1-66.3 minutes)" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
214 <has_text text="Mass range: 300-400 m/z" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
215 <has_text text="Peaks: 1311 (about 328 per sample)" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
216 <has_text text="Peak Groups: 0" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
217 <has_text text="Sample classes: KO, WT" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
218 </assert_stdout>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
219 </test>-->
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
220 <test>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
221 <param name="image" value="ko15-raw.RData" ftype="rdata" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
222 <conditional name="methods">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
223 <param name="method" value="CentWave" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
224 <param name="ppm" value="25" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
225 <param name="peakwidth" value="20,50" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
226 </conditional>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
227 <expand macro="test_file_load_single_ko15"/>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
228 <assert_stdout>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
229 <has_text text="ppm: 25" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
230 <has_text text="peakwidth: 20, 50" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
231 <has_text text="object with 1 samples" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
232 <has_text text="Time range: 2506.1-4471.7 seconds (41.8-74.5 minutes)" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
233 <has_text text="Mass range: 200.2-600 m/z" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
234 <has_text text="Peaks: 2262 (about 2262 per sample)" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
235 <has_text text="Peak Groups: 0" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
236 <has_text text="Sample classes: ." />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
237 </assert_stdout>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
238 </test>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
239 <!-- DISABLE FOR TRAVIS
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
240 Useful to generate test-data for the further steps
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
241 <test>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
242 <param name="image" value="ko16-raw.RData" ftype="rdata" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
243 <conditional name="methods">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
244 <param name="method" value="CentWave" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
245 <param name="ppm" value="25" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
246 <param name="peakwidth" value="20,50" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
247 </conditional>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
248 <assert_stdout>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
249 <has_text text="object with 1 samples" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
250 <has_text text="Time range: 2521.7-4477.9 seconds (42-74.6 minutes)" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
251 <has_text text="Mass range: 200.1-600 m/z" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
252 <has_text text="Peaks: 2408 (about 2408 per sample)" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
253 <has_text text="Peak Groups: 0" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
254 <has_text text="Sample classes: ." />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
255 </assert_stdout>
7
451ff602a957 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
256 </test>
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
257 <test>
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
258 <param name="image" value="wt15-raw.RData" ftype="rdata" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
259 <conditional name="methods">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
260 <param name="method" value="CentWave" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
261 <param name="ppm" value="25" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
262 <param name="peakwidth" value="20,50" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
263 </conditional>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
264 <assert_stdout>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
265 <has_text text="object with 1 samples" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
266 <has_text text="Time range: 2517-4473.2 seconds (42-74.6 minutes)" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
267 <has_text text="Mass range: 200.2-599.8 m/z" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
268 <has_text text="Peaks: 2278 (about 2278 per sample)" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
269 <has_text text="Peak Groups: 0" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
270 <has_text text="Sample classes: ." />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
271 </assert_stdout>
12
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
272 </test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
273 <test>
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
274 <param name="image" value="wt16-raw.RData" ftype="rdata" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
275 <conditional name="methods">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
276 <param name="method" value="CentWave" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
277 <param name="ppm" value="25" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
278 <param name="peakwidth" value="20,50" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
279 </conditional>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
280 <assert_stdout>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
281 <has_text text="object with 1 samples" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
282 <has_text text="Time range: 2521.7-4468.5 seconds (42-74.5 minutes)" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
283 <has_text text="Mass range: 200.3-600 m/z" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
284 <has_text text="Peaks: 2303 (about 2303 per sample)" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
285 <has_text text="Peak Groups: 0" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
286 <has_text text="Sample classes: ." />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
287 </assert_stdout>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
288 </test>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
289 -->
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
290 <!-- DISABLE FOR TRAVIS
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
291 Test to test the different methods parameters
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
292 <test>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
293 <param name="image" value="ko15-raw.RData" ftype="rdata" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
294 <conditional name="methods">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
295 <param name="method" value="MatchedFilter" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
296 <param name="fwhm" value="35" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
297 <section name="MatchedFilterAdv"
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
298 <conditional name="impute_cond">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
299 <param name="impute" value="linbase" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
300 <param name="baseValue" value="0.1" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
301 <param name="distance" value="1" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
302 </conditional>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
303 </section>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
304 </conditional>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
305 <assert_stdout>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
306 <has_text text="fwhm: 35" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
307 <has_text text="impute: linbase" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
308 <has_text text="baseValue: 0.1" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
309 <has_text text="distance: 1" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
310 </assert_stdout>
12
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
311 </test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
312 <test>
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
313 <param name="image" value="ko15-raw.RData" ftype="rdata" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
314 <conditional name="methods">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
315 <param name="method" value="CentWavePredIso" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
316 <param name="ppm" value="56" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
317 <param name="peakwidth" value="5.275,13.5" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
318 <section name="CentWaveAdvROI">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
319 <param name="roiList" value="roiList.txt" ftype="tabular" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
320 </section>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
321 </conditional>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
322 <assert_stdout>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
323 <has_text text=" scmin scmax mzmin mzmax length intensity" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
324 <has_text text="1 200 300 300 350 100 5000" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
325 </assert_stdout>
12
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
326 </test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
327 <test>
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
328 <param name="image" value="ko15-raw.RData" ftype="rdata" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
329 <conditional name="methods">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
330 <param name="method" value="MSW" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
331 <param name="snthresh" value="4" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
332 <param name="verboseColumns" value="true" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
333 </conditional>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
334 <assert_stdout>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
335 <has_text text="snthresh: 4" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
336 <has_text text="verboseColumns: TRUE" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
337 </assert_stdout>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
338 </test>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
339 -->
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
340 <!-- DISABLE FOR TRAVIS
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
341 No more test-data/sacuri_dir_root.zip
12
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
342 <test>
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
343 <param name="image" value="sacuri_dir_root.zip" ftype="zip" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
344 <conditional name="methods">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
345 <param name="method" value="MatchedFilter" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
346 <param name="step" value="0.01" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
347 <param name="fwhm" value="4" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
348 <conditional name="options_m">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
349 <param name="option" value="show" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
350 <param name="max" value="50" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
351 <param name="snthresh" value="1" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
352 <param name="steps" value="2" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
353 </conditional>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
354 </conditional>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
355 <assert_stdout>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
356 <has_text text="object with 4 samples" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
357 <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
358 <has_text text="Mass range: 50.0021-999.9863 m/z" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
359 <has_text text="Peaks: 59359 (about 14840 per sample)" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
360 <has_text text="Peak Groups: 0" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
361 <has_text text="Sample classes: bio, blank" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
362 </assert_stdout>
12
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
363 </test>
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
364 -->
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
365 <!-- DISABLE FOR TRAVIS
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
366 No more test-data/sacuri_current_root.zip
12
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
367 <test>
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
368 <param name="image" value="sacuri_current_root.zip" ftype="zip" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
369 <conditional name="methods">
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
370 <param name="method" value="CentWave" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
371 <param name="ppm" value="25" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
372 <param name="peakwidth" value="20,50" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
373 </conditional>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
374 <assert_stdout>
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
375 <has_text text="object with 4 samples" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
376 <has_text text="Time range: 3.5-1139.2 seconds (0.1-19 minutes)" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
377 <has_text text="Mass range: 57.9756-593.4086 m/z" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
378 <has_text text="Peaks: 1535 (about 384 per sample)" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
379 <has_text text="Peak Groups: 0" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
380 <has_text text="Sample classes: bio, blank" />
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
381 </assert_stdout>
12
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
382 </test>
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
383 -->
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
384 </tests>
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
385
5
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
386 <help><![CDATA[
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
387
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
388 @HELP_AUTHORS@
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
389
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
390 ===================
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
391 xcms findChromPeaks
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
392 ===================
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
393
054e4681667c planemo upload
lecorguille
parents:
diff changeset
394 -----------
054e4681667c planemo upload
lecorguille
parents:
diff changeset
395 Description
054e4681667c planemo upload
lecorguille
parents:
diff changeset
396 -----------
054e4681667c planemo upload
lecorguille
parents:
diff changeset
397
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
398 This tool is used for preprocessing data from multiple LC/MS files (NetCDF, mzXML and mzData formats) using the xcms_ R package. It extracts ions from each sample independently, and using a statistical model, peaks are filtered and integrated.
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
399 A tutorial on how to perform xcms preprocessing is available here_.
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
400
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
401 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
402 .. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf
054e4681667c planemo upload
lecorguille
parents:
diff changeset
403
054e4681667c planemo upload
lecorguille
parents:
diff changeset
404
054e4681667c planemo upload
lecorguille
parents:
diff changeset
405 -----------------
054e4681667c planemo upload
lecorguille
parents:
diff changeset
406 Workflow position
054e4681667c planemo upload
lecorguille
parents:
diff changeset
407 -----------------
054e4681667c planemo upload
lecorguille
parents:
diff changeset
408
054e4681667c planemo upload
lecorguille
parents:
diff changeset
409 **Upstream tools**
054e4681667c planemo upload
lecorguille
parents:
diff changeset
410
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
411 ========================= ================= ==============================
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
412 Name Output file Format
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
413 ========================= ================= ==============================
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
414 MSnbase.readMSData ``*``.raw.RData rdata.msnbase.raw
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
415 ========================= ================= ==============================
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
416
054e4681667c planemo upload
lecorguille
parents:
diff changeset
417
054e4681667c planemo upload
lecorguille
parents:
diff changeset
418 **Downstream tools**
054e4681667c planemo upload
lecorguille
parents:
diff changeset
419
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
420 ==================================== ======================== =========================
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
421 Name Output file Format
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
422 ==================================== ======================== =========================
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
423 xcms.findChromPeaks Merger (single) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
424 ------------------------------------ ------------------------ -------------------------
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
425 xcms.groupChromPeaks (zip) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
426 ==================================== ======================== =========================
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
427
054e4681667c planemo upload
lecorguille
parents:
diff changeset
428
054e4681667c planemo upload
lecorguille
parents:
diff changeset
429 **Example of a metabolomic workflow**
054e4681667c planemo upload
lecorguille
parents:
diff changeset
430
12
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
431 .. image:: xcms_xcmsset_workflow.png
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
432
054e4681667c planemo upload
lecorguille
parents:
diff changeset
433 ---------------------------------------------------
054e4681667c planemo upload
lecorguille
parents:
diff changeset
434
054e4681667c planemo upload
lecorguille
parents:
diff changeset
435 ----------
054e4681667c planemo upload
lecorguille
parents:
diff changeset
436 Parameters
054e4681667c planemo upload
lecorguille
parents:
diff changeset
437 ----------
054e4681667c planemo upload
lecorguille
parents:
diff changeset
438
054e4681667c planemo upload
lecorguille
parents:
diff changeset
439 Extraction method for peaks detection
054e4681667c planemo upload
lecorguille
parents:
diff changeset
440 -------------------------------------
054e4681667c planemo upload
lecorguille
parents:
diff changeset
441
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
442 **MatchedFilter**
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
443
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
444 | The matchedFilter algorithm identifies peaks in the chromatographic time domain as described in [Smith 2006]. The intensity values are binned by cutting The LC/MS data into slices (bins) of a mass unit (‘binSize’ m/z) wide. Within each bin the maximal intensity is selected. The chromatographic peak detection is then performed in each bin by extending it based on the ‘steps’ parameter to generate slices comprising bins ‘current_bin - steps +1’ to ‘current_bin + steps - 1’. Each of these slices is then filtered with matched filtration using a second-derative Gaussian as the model peak shape. After filtration peaks are detected using a signal-to-ratio cut-off. For more details and illustrations see [Smith 2006].
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
445 | See the MatchedFilter_manual_
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
446
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
447 **CentWave**
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
448
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
449 | The centWave algorithm perform peak density and wavelet based chromatographic peak detection for high resolution LC/MS data in centroid mode [Tautenhahn 2008].
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
450 | Due to the fact that peak centroids are used, a binning step is not necessary.
054e4681667c planemo upload
lecorguille
parents:
diff changeset
451 | The method is capable of detecting close-by-peaks and also overlapping peaks. Some efforts are made to detect the exact peak boundaries to get precise peak integrals.
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
452 | See the CentWave_manual_
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
453
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
454 **CentWaveWithPredIsoROIs**
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
455
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
456 | This method performs a two-step centWave-based chromatographic peak detection: in a first centWave run peaks are identified for which then the location of their potential isotopes in the mz-retention time is predicted. A second centWave run is then performed on these regions of interest (ROIs). The final list of chromatographic peaks comprises all non-overlapping peaks from both centWave runs.
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
457 | See the CentWaveWithPredIsoROIs_manual_
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
458
054e4681667c planemo upload
lecorguille
parents:
diff changeset
459 **MSW**
054e4681667c planemo upload
lecorguille
parents:
diff changeset
460
054e4681667c planemo upload
lecorguille
parents:
diff changeset
461 | Wavelet based, used for direct infusion data. Continuous wavelet transform (CWT) can be used to locate chromatographic peaks on different scales.
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
462 | See the MSW_manual_
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
463
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
464 .. _MatchedFilter_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-matchedFilter.html#heading-2
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
465 .. _CentWave_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-centWave.html#heading-2
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
466 .. _CentWaveWithPredIsoROIs_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-centWaveWithPredIsoROIs.html#heading-2
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
467 .. _MSW_manual: https://rdrr.io/bioc/xcms/man/findPeaks-MSW.html#heading-2
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
468
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
469 @HELP_XCMS_MANUAL@
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
470
054e4681667c planemo upload
lecorguille
parents:
diff changeset
471 ------------
054e4681667c planemo upload
lecorguille
parents:
diff changeset
472 Output files
054e4681667c planemo upload
lecorguille
parents:
diff changeset
473 ------------
054e4681667c planemo upload
lecorguille
parents:
diff changeset
474
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
475 xset.RData: rdata.xcms.findchrompeaks format
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
476
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
477 | (single) RData files that are necessary in the second step of the workflow "xcms.groupChromPeaks" - must be merged first using "xcms.findChromPeaks Merger"
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
478 | (zip) RData file that is necessary in the second step of the workflow "xcms.groupChromPeaks".
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
479
5
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
480 ---------------------------------------------------
4
c5fa73f1703f Uploaded
mmonsoor
parents: 0
diff changeset
481
5
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
482 Changelog/News
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
483 --------------
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
484
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
485
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
486 **Version 3.0.0.0 - 08/03/2018**
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
487
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
488 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed.
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
489
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
490 - CHANGE: xcms.findChromPeaks no longer read the raw data. You have to run MSnbase readMSData first.
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
491
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
492 - NEW: a bunch of new options: Spectra Filters (previously scanrange), CentWave.(mzCenterFun, fitgauss, verboseColumns), MatchedFilter.(sigma, impute, baseValue, max), MSW.(verboseColumns), ...
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
493
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
494 - NEW: new Filters for Spectra
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
495
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
496 - NEW: new methods: CentWaveWithPredIsoROIs
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
497
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
498 - UPDATE: since xcms 3.0.0, some options are no more available: scanrange (replace by filters), profmethod, MatchedFilter.step, MatchedFilter.sigma, MSW.winSize.noise, MSW.SNR.method
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
499
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
500 - IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values.
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
501
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
502 - IMPROVEMENT: the tool "should" be now more flexible in term of file naming: it "should" accept space and comma. But don't be too imaginative :)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
503
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
504 - CHANGE: removing of the TIC and BPC plots. You can new use the dedicated tool "xcms plot chromatogram"
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
505
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
506
13
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
507 **Version 2.1.1 - 29/11/2017**
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
508
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
509 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
510
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
511
12
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
512 **Version 2.1.0 - 22/02/2017**
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
513
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
514 - NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group".
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
515
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
516 - BUGFIX: the default value of "matchedFilter" -> "Step size to use for profile generation" which was of 0.01 have been changed to fix with the XMCS default values to 0.1
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
517
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
518
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
519 **Version 2.0.11 - 22/12/2016**
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
520
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
521 - BUGFIX: propose scanrange for all methods
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
522
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
523
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
524 **Version 2.0.10 - 22/12/2016**
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
525
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
526 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
527
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
528
10
69eb0fc05837 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 7
diff changeset
529 **Version 2.0.9 - 06/07/2016**
69eb0fc05837 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 7
diff changeset
530
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
531 - UPGRADE: upgrade the xcms version from 1.44.0 to 1.46.0
10
69eb0fc05837 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 7
diff changeset
532
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
533
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
534 **Version 2.0.8 - 06/04/2016**
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
535
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
536 - TEST: refactoring to pass planemo test using conda dependencies
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
537
5
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
538
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
539 **Version 2.0.7 - 10/02/2016**
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
540
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
541 - BUGFIX: better management of errors. Datasets remained green although the process failed
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
542
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
543 - BUGFIX/IMPROVEMENT: New checking steps around the imported data in order to raise explicte error message before or after launch XCMS: checking of bad characters in the filenames, checking of the XML integrity and checking of duplicates which can appear in the sample names during the XCMS process because of bad characters
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
544
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
545 - BUGFIX/IMPROVEMENT: New step to check and delete bad characters in the XML: accented characters in the storage path of the mass spectrometer
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
546
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
547 - UPDATE: refactoring of internal management of inputs/outputs
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
548
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
549 - TEST: refactoring to feed the new report tool
5
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
550
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
551
13
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
552 **Version 2.0.2 - 18/01/2016**
5
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
553
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
554 - BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
555
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
556
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
557 **Version 2.0.2 - 09/10/2015**
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
558
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
559 - BUGFIX: Some users reported a bug in xcms.xcmsSet. The preprocessing stops itself and doesn't import the whole dataset contained in the zip file without warning. But meanwhile, please check your samplemetadata dataset and the number of rows.
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
560
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
561
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
562 **Version 2.0.2 - 02/06/2015**
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
563
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
564 - NEW: The W4M workflows will now take as input a zip file to ease the transfer and to improve dataset exchange between tools and users. (See How_to_upload). The previous "Library directory name" is still available but we invite user to switch on the new zip system as soon as possible.
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
565
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
566 - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
567
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
568 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
569
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
570 ]]></help>
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
571
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
572 <expand macro="citation" />
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
573 </tool>