annotate abims_xcms_group.xml @ 21:2d94a873d649 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4632d03b53c344757d71dd3310d37069fb498b26
author lecorguille
date Tue, 12 Mar 2019 11:03:30 -0400
parents 63d9c5980c07
children 761913919c21
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
19
c8f8d598f562 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
lecorguille
parents: 18
diff changeset
1 <tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@WRAPPER_VERSION@.0">
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
2
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
3 <description>Perform the correspondence, the grouping of chromatographic peaks within and between samples.</description>
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
4
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
5 <macros>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
6 <import>macros.xml</import>
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
7 <import>macros_xcms.xml</import>
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
8 </macros>
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
9
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
10 <expand macro="requirements"/>
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
11 <expand macro="stdio"/>
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
12
3
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
13 <command><![CDATA[
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
14 @COMMAND_RSCRIPT@/xcms_group.r
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
15 image '$image'
3
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
16
13
13558e8a4778 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
17 method $methods.method
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
18 #if $methods.method == "PeakDensity":
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
19 bw $methods.bw
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
20 minFraction $methods.minFraction
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
21 minSamples $methods.minSamples
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
22 binSize $methods.binSize
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
23 ## Advanced
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
24 maxFeatures $methods.PeakDensityAdv.maxFeatures
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
25 #elif $methods.method == "MzClust":
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
26 ppm $methods.ppm
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
27 absMz $methods.absMz
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
28 minFraction $methods.minFraction
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
29 minSamples $methods.minSamples
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
30 #else:
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
31 mzVsRtBalance $methods.mzVsRtBalance
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
32 absMz $methods.absMz
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
33 absRt $methods.absRt
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
34 kNN $methods.kNN
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
35 #end if
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
36
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
37 @COMMAND_PEAKLIST@
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
38
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
39 @COMMAND_FILE_LOAD@
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
40
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
41 @COMMAND_LOG_EXIT@
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
42 ]]></command>
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
43
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
44 <inputs>
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
45 <param name="image" type="data" format="rdata.xcms.findchrompeaks,rdata.xcms.group,rdata.xcms.retcor,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks or adjustRtime" />
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
46 <conditional name="methods">
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
47 <param name="method" type="select" label="Method to use for grouping" help="See the help section below">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
48 <option value="PeakDensity" selected="true">PeakDensity - peak grouping based on time dimension peak densities</option>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
49 <option value="MzClust">MzClust - high resolution peak grouping for single spectra (direct infusion) MS data</option>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
50 <option value="NearestPeaks">NearestPeaks - chromatographic peak grouping based on their proximity in the mz-rt space</option>
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
51 </param>
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
52 <when value="PeakDensity">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
53 <param argument="bw" type="float" value="30" label="Bandwidth" help="bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
54 <param argument="minFraction" type="float" value="0.5" label="Minimum fraction of samples" help="in at least one sample group in which the peaks have to be present to be considered as a peak group (feature)" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
55 <param argument="minSamples" type="integer" value="1" label="Minimum number of samples" help="in at least one sample group in which the peaks have to be detected to be considered a peak group (feature)" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
56 <param argument="binSize" type="float" value="0.25" label="Width of overlapping m/z slices" help="to use for creating peak density chromatograms and grouping peaks across samples (previously mzdiff)" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
57
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
58 <section name="PeakDensityAdv" title="Advanced Options" expanded="False">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
59 <param argument="maxFeatures" type="integer" value="50" label="Maximum number of groups to identify in a single m/z slice" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
60 </section>
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
61 </when>
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
62 <when value="MzClust">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
63 <param argument="ppm" type="integer" value="20" label="Relative mz error for clustering/grouping in ppm" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
64 <param argument="absMz" type="float" value="0" label="Absolute mz error for clustering/grouping" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
65 <param argument="minFraction" type="float" value="0.5" label="Minimum fraction of samples" help="in at least one sample group in which the peaks have to be present to be considered as a peak group (feature)" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
66 <param argument="minSamples" type="integer" value="1" label="Minimum number of samples" help="in at least one sample group in which the peaks have to be detected to be considered a peak group (feature)" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
67 </when>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
68 <when value="NearestPeaks">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
69 <param argument="mzVsRtBalance" type="integer" value="10" label="Factor by which mz values are multiplied before calculating the (euclician) distance between two peaks" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
70 <param argument="absMz" type="float" value="0.2" label="Maximum tolerated distance for mz values" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
71 <param argument="absRt" type="integer" value="15" label="Maximum tolerated distance for RT values" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
72 <param argument="kNN" type="integer" value="10" label="Number of nearest Neighbours to check" />
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
73 </when>
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
74 </conditional>
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
75
17
95e689b7f27f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 878be1bfbe93af0a140df76fa47f0a82a48189e3
lecorguille
parents: 14
diff changeset
76 <expand macro="input_peaklist_conditional"/>
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
77
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
78 <expand macro="input_file_load"/>
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
79 </inputs>
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
80
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
81 <outputs>
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
82 <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.groupChromPeaks.RData" from_work_dir="group.RData"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
83 <data name="plotChromPeakDensity" format="pdf" label="${image.name[:-6]}.groupChromPeaks.plotChromPeakDensity.pdf" from_work_dir="plotChromPeakDensity.pdf"/>
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
84 <expand macro="output_peaklist" function="group"/>
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
85 </outputs>
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
86
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
87 <tests>
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
88 <!-- from xcmsSet
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
89 <test>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
90 <param name="image" value="faahKO-single-class.xset.merged.RData" ftype="rdata"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
91 <conditional name="methods">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
92 <param name="method" value="PeakDensity"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
93 <param name="bw" value="5"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
94 <param name="minFraction" value="0.3"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
95 <param name="binSize" value="0.01"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
96 <section name="PeakDensityAdv">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
97 <param name="maxFeatures" value="50"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
98 </section>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
99 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
100 <conditional name="peaklist">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
101 <param name="peaklistBool" value="true" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
102 <param name="convertRTMinute" value="false" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
103 <param name="numDigitsMZ" value="4" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
104 <param name="numDigitsRT" value="1" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
105 <param name="naTOzero" value="false" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
106 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
107 <expand macro="test_file_load_single"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
108 <assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
109 <has_text text="bw: 5" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
110 <has_text text="minFraction: 0.3" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
111 <has_text text="maxFeatures: 50" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
112 <has_text text="object with 4 samples" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
113 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
114 <has_text text="Mass range: 200.1-600 m/z" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
115 <has_text text="Peaks: 9251 (about 2313 per sample)" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
116 <has_text text="Peak Groups: 8372" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
117 <has_text text="Sample classes: KO, WT" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
118 </assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
119 <output name="variableMetadata" file="faahKO.xset.group.variableMetadata.tsv" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
120 <output name="dataMatrix" file="faahKO.xset.group.dataMatrix.tsv" />
5
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 4
diff changeset
121 </test>-->
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
122 <!-- DISABLE FOR TRAVIS
5
0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 4
diff changeset
123 <test>
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
124 <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
125 <conditional name="methods">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
126 <param name="method" value="PeakDensity"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
127 <param name="bw" value="5"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
128 <param name="minFraction" value="0.3"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
129 <param name="binSize" value="0.01"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
130 <conditional name="density_options">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
131 <param name="option" value="show"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
132 <param name="maxFeatures" value="50"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
133 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
134 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
135 <expand macro="test_file_load_single"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
136 <assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
137 <has_text text="object with 4 samples" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
138 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
139 <has_text text="Mass range: 200.1-600 m/z" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
140 <has_text text="Peaks: 9251 (about 2313 per sample)" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
141 <has_text text="Peak Groups: 611" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
142 <has_text text="Sample classes: ." />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
143 </assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
144 </test>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
145 -->
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
146 <!-- DISABLE FOR TRAVIS Zip from xcmsSet
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
147 <test>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
148 <param name="image" value="faahKO.xset.RData" ftype="rdata"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
149 <conditional name="methods">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
150 <param name="method" value="PeakDensity"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
151 <param name="bw" value="5"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
152 <param name="minFraction" value="0.3"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
153 <param name="binSize" value="0.01"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
154 <conditional name="density_options">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
155 <param name="option" value="show"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
156 <param name="maxFeatures" value="50"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
157 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
158 </conditional>
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
159 <conditional name="peaklist">
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
160 <param name="convertRTMinute" value="false" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
161 <param name="peaklistBool" value="true" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
162 <param name="numDigitsMZ" value="4" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
163 <param name="numDigitsRT" value="1" />
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
164 <param name="naTOzero" value="false" />
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
165 </conditional>
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
166 <expand macro="test_file_load_zip"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
167 <assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
168 <has_text text="object with 4 samples" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
169 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
170 <has_text text="Mass range: 200.1-600 m/z" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
171 <has_text text="Peaks: 9251 (about 2313 per sample)" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
172 <has_text text="Peak Groups: 8372" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
173 <has_text text="Sample classes: KO, WT" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
174 </assert_stdout>
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
175 <output name="variableMetadata" file="faahKO.xset.group.variableMetadata.tsv" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
176 <output name="dataMatrix" file="faahKO.xset.group.dataMatrix.tsv" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
177 </test>
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
178 -->
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
179
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
180 <!-- DISABLE FOR TRAVIS Zip from retcor
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
181 <test>
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
182 <param name="image" value="faahKO.xset.group.retcor.RData" ftype="rdata"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
183 <conditional name="methods">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
184 <param name="method" value="PeakDensity"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
185 <param name="bw" value="5"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
186 <param name="minFraction" value="0.3"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
187 <param name="binSize" value="0.01"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
188 <conditional name="density_options">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
189 <param name="option" value="show"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
190 <param name="maxFeatures" value="50"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
191 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
192 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
193 <expand macro="test_file_load_zip"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
194 <assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
195 <has_text text="object with 4 samples" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
196 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
197 <has_text text="Mass range: 200.1-600 m/z" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
198 <has_text text="Peaks: 9251 (about 2313 per sample)" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
199 <has_text text="Peak Groups: 8209" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
200 <has_text text="Sample classes: KO, WT" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
201 </assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
202 </test>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
203 -->
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
204 <!-- from retcor -->
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
205 <test>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
206 <param name="image" value="faahKO-single.xset.merged.group.retcor.RData" ftype="rdata"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
207 <conditional name="methods">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
208 <param name="method" value="PeakDensity"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
209 <param name="bw" value="5"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
210 <param name="minFraction" value="0.3"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
211 <param name="binSize" value="0.01"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
212 <section name="PeakDensityAdv">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
213 <param name="maxFeatures" value="50"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
214 </section>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
215 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
216 <expand macro="test_file_load_single"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
217 <assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
218 <has_text text="bw: 5" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
219 <has_text text="minFraction: 0.3" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
220 <has_text text="binSize: 0.01"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
221 <has_text text="maxFeatures: 50" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
222 <has_text text="object with 4 samples" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
223 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
224 <has_text text="Mass range: 200.1-600 m/z" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
225 <has_text text="Peaks: 9251 (about 2313 per sample)" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
226 <has_text text="Peak Groups: 8209" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
227 <has_text text="Sample classes: KO, WT" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
228 </assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
229 </test>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
230 <!-- DISABLE FOR TRAVIS
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
231 Test to test the different methods parameters
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
232 <test expect_failure="True">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
233 <param name="image" value="faahKO-single.xset.merged.group.retcor.RData" ftype="rdata"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
234 <conditional name="methods">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
235 <param name="method" value="MzClust"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
236 <param name="ppm" value="21"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
237 <param name="absMz" value="0.1"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
238 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
239 <expand macro="test_file_load_single"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
240 <assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
241 <has_text text="ppm: 21" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
242 <has_text text="absMz: 0.1" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
243 </assert_stdout>
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
244 </test>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
245 <test>
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
246 <param name="image" value="faahKO-single.xset.merged.group.retcor.RData" ftype="rdata"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
247 <conditional name="methods">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
248 <param name="method" value="NearestPeaks"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
249 <param name="mzVsRtBalance" value="11"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
250 <param name="absMz" value="0.1"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
251 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
252 <expand macro="test_file_load_single"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
253 <assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
254 <has_text text="mzVsRtBalance: 11" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
255 <has_text text="absMz: 0.1" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
256 </assert_stdout>
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
257 </test>
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
258 -->
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
259 </tests>
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
260
3
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
261 <help><![CDATA[
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
262
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
263 @HELP_AUTHORS@
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
264
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
265 ====================
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
266 xcms groupChromPeaks
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
267 ====================
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
268
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
269 -----------
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
270 Description
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
271 -----------
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
272
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
273 After peak identification with xcmsSet, this tool groups the peaks which represent the same analyte across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time. Allows rejection of features, which are only partially detected within the replicates of a sample class.
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
274
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
275 -----------------
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
276 Workflow position
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
277 -----------------
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
278
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
279 **Upstream tools**
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
280
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
281 ==================================== ======================== ==============================
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
282 Name Output file Format
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
283 ==================================== ======================== ==============================
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
284 xcms.findChromPeaks Merger (single) xset.merged.RData rdata.xcms.findchrompeaks
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
285 ------------------------------------ ------------------------ ------------------------------
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
286 xcms.findChromPeaks (zip) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
287 ------------------------------------ ------------------------ ------------------------------
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
288 xcms.adjustRtime ``*``.adjustRtime.RData rdata.xcms.retcor
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
289 ==================================== ======================== ==============================
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
290
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
291
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
292 **Downstream tools**
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
293
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
294 =========================== =========================== ====================
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
295 Name Output file Format
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
296 =========================== =========================== ====================
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
297 xcms.adjustRtime ``*``.groupChromPeaks.RData rdata.xcms.group
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
298 --------------------------- --------------------------- --------------------
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
299 xcms.fillChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
300 =========================== =========================== ====================
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
301
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
302 **General schema of the metabolomic workflow**
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
303
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
304 .. image:: xcms_group_workflow.png
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
305
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
306 ---------------------------------------------------
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
307
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
308 ----------
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
309 Parameters
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
310 ----------
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
311
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
312 Method to use for grouping
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
313 --------------------------
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
314
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
315 **MzClust**
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
316
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
317 | This method performs high resolution correspondence for single spectra samples.
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
318 | See the MzClust_manual_
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
319
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
320 **PeakDensity**
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
321
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
322 | This method performs performs correspondence (chromatographic peak grouping) based on the density (distribution) of identified peaks along the retention time axis within slices of overlapping mz ranges. All peaks (from the same or from different samples) being close on the retention time axis are grouped into a feature (peak group).
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
323 | See the PeakDensity_manual_
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
324
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
325 **NearestPeaks**
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
326
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
327 | This method is inspired by the grouping algorithm of mzMine [Katajamaa 2006] and performs correspondence based on proximity of peaks in the space spanned by retention time and mz values. The method creates first a master peak list consisting of all chromatographic peaks from the sample in which most peaks were identified, and starting from that, calculates distances to peaks from the sample with the next most number of peaks. If peaks are closer than the defined threshold they are grouped together.
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
328 | See the NearestPeaks_manual_
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
329
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
330 .. _MzClust_manual: https://rdrr.io/bioc/xcms/man/groupChromPeaks-mzClust.html#heading-2
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
331 .. _PeakDensity_manual: https://rdrr.io/bioc/xcms/man/groupChromPeaks-density.html#heading-2
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
332 .. _NearestPeaks_manual: https://rdrr.io/bioc/xcms/man/groupChromPeaks-nearest.html#heading-2
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
333
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
334 @HELP_XCMS_MANUAL@
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
335
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
336 @HELP_PEAKLIST@
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
337
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
338 ------------
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
339 Output files
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
340 ------------
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
341
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
342 xset.groupChromPeaks.RData: rdata.xcms.group format
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
343
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
344 | RData file that will be necessary in the third and fourth step of the workflow (xcms.adjustRtime and xcms.fillChromPeaks).
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
345
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
346 xset.groupChromPeaks.plotChromPeakDensity.pdf
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
347
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
348 | Density plot
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
349
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
350 @HELP_PEAKLIST_OUTPUT@
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
351
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
352
3
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
353 ---------------------------------------------------
2
ed149026836e Uploaded
mmonsoor
parents: 0
diff changeset
354
3
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
355 Changelog/News
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
356 --------------
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
357
20
63d9c5980c07 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9
lecorguille
parents: 19
diff changeset
358 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
19
c8f8d598f562 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
lecorguille
parents: 18
diff changeset
359
20
63d9c5980c07 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9
lecorguille
parents: 19
diff changeset
360 **Version 3.4.4.0 - 08/02/2019**
63d9c5980c07 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9
lecorguille
parents: 19
diff changeset
361
63d9c5980c07 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9
lecorguille
parents: 19
diff changeset
362 - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_)
19
c8f8d598f562 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
lecorguille
parents: 18
diff changeset
363
c8f8d598f562 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
lecorguille
parents: 18
diff changeset
364 - BUGFIX: groupChromPeaks wasn't pass to the ChromPeakDensity plots
c8f8d598f562 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
lecorguille
parents: 18
diff changeset
365
c8f8d598f562 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
lecorguille
parents: 18
diff changeset
366 - BUGFIX: issue with Inf values in the exported DataMatrix: https://github.com/sneumann/xcms/issues/323#issuecomment-433044378
c8f8d598f562 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
lecorguille
parents: 18
diff changeset
367
18
7a19925478e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989
lecorguille
parents: 17
diff changeset
368 **Version 3.0.0.1 - 09/11/2018**
7a19925478e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989
lecorguille
parents: 17
diff changeset
369
7a19925478e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989
lecorguille
parents: 17
diff changeset
370 - BUGFIX: issue when the vector at peakidx is too long and is written in a new line during the export of the peaklist
7a19925478e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989
lecorguille
parents: 17
diff changeset
371
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
372 **Version 3.0.0.0 - 08/03/2018**
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
373
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
374 - 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.
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
375
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
376 - NEW: a bunch of new options: PeakDensity.minSamples), MzClust.minSamples)
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
377
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
378 - NEW: a new density plot
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
379
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
380 - IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values.
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
381
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
382
13
13558e8a4778 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
383 **Version 2.1.1 - 29/11/2017**
13558e8a4778 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
384
13558e8a4778 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
385 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
13558e8a4778 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
386
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
387
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
388 **Version 2.1.0 - 07/02/2017**
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
389
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
390 - IMPROVEMENT: Add an option to export the peak list at this step without have to wait camara.annotate
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
391
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
392 - IMPROVEMENT: xcms.group can deal with merged individual data from "xcms.xcmsSet Merger"
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
393
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
394 - BUGFIX: the default value of "density" -> "Maximum number of groups to identify in a single m/z slice" which was of 5 have been changed to fix with the XMCS default values to 50
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
395
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
396
8
5d80e7511dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 5
diff changeset
397 **Version 2.0.6 - 06/07/2016**
5d80e7511dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 5
diff changeset
398
5d80e7511dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 5
diff changeset
399 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
5d80e7511dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 5
diff changeset
400
14
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
401
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
402 **Version 2.0.5 - 04/04/2016**
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
403
10
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 8
diff changeset
404 - TEST: refactoring to pass planemo test using conda dependencies
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
405
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
406
3
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
407 **Version 2.0.4 - 10/02/2016**
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
408
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
409 - BUGFIX: better management of errors. Datasets remained green although the process failed
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
410
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
411 - UPDATE: refactoring of internal management of inputs/outputs
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
412
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
413 - UPDATE: refactoring to feed the new report tool
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
414
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
415
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
416 **Version 2.0.2 - 02/06/2015**
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
417
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
418 - 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.
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
419
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
420 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
421
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
422
98e33cdf0eb1 planemo upload
lecorguille
parents: 2
diff changeset
423 ]]></help>
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
424
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
425
4
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
426 <expand macro="citation" />
0
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
427
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
428
f3f97841564f Uploaded
lecorguille
parents:
diff changeset
429 </tool>