xcms_group: abims_xcms_group.xml annotate

annotate abims_xcms_group.xml @ 30:3820e3f3b1cb draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163

author	workflow4metabolomics
date	Mon, 03 Feb 2025 14:45:05 +0000
parents	2b676d5eb848
children

rev	line source
28 2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e workflow4metabolomics parents: 27 diff changeset	1 <tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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"/>
30 3820e3f3b1cb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163 workflow4metabolomics parents: 28 diff changeset	11 <required_files>
3820e3f3b1cb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163 workflow4metabolomics parents: 28 diff changeset	12 <include path="xcms_group.r" />
3820e3f3b1cb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163 workflow4metabolomics parents: 28 diff changeset	13 <include path="lib.r" />
3820e3f3b1cb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163 workflow4metabolomics parents: 28 diff changeset	14 </required_files>
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	15 <expand macro="stdio"/>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	16
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	17 <command><![CDATA[
30 3820e3f3b1cb planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163 workflow4metabolomics parents: 28 diff changeset	18 @COMMAND_RSCRIPT@xcms_group.r
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	19 image '$image'
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	20
13 13558e8a4778 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	21 method $methods.method
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	22 #if $methods.method == "PeakDensity":
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	23 bw $methods.bw
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	24 minFraction $methods.minFraction
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	25 minSamples $methods.minSamples
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	26 binSize $methods.binSize
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	27 ## Advanced
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	28 maxFeatures $methods.PeakDensityAdv.maxFeatures
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	29 #elif $methods.method == "MzClust":
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	30 ppm $methods.ppm
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	31 absMz $methods.absMz
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	32 minFraction $methods.minFraction
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	33 minSamples $methods.minSamples
0 f3f97841564f Uploaded lecorguille parents: diff changeset	34 #else:
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	35 mzVsRtBalance $methods.mzVsRtBalance
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	36 absMz $methods.absMz
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	37 absRt $methods.absRt
0 f3f97841564f Uploaded lecorguille parents: diff changeset	38 kNN $methods.kNN
f3f97841564f Uploaded lecorguille parents: diff changeset	39 #end if
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	40
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	41 @COMMAND_PEAKLIST@
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	42
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	43 @COMMAND_FILE_LOAD@
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	44
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	45 @COMMAND_LOG_EXIT@
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	46 ]]></command>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	47
f3f97841564f Uploaded lecorguille parents: diff changeset	48 <inputs>
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	49 <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	50 <conditional name="methods">
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	51 <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	52 <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	53 <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	54 <option value="NearestPeaks">NearestPeaks - chromatographic peak grouping based on their proximity in the mz-rt space</option>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	55 </param>
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	56 <when value="PeakDensity">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	57 <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	58 <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	59 <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	60 <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	61
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	62 <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	63 <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	64 </section>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	65 </when>
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	66 <when value="MzClust">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	67 <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	68 <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	69 <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	70 <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	71 </when>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	72 <when value="NearestPeaks">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	73 <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	74 <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	75 <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	76 <param argument="kNN" type="integer" value="10" label="Number of nearest Neighbours to check" />
0 f3f97841564f Uploaded lecorguille parents: diff changeset	77 </when>
f3f97841564f Uploaded lecorguille parents: diff changeset	78 </conditional>
f3f97841564f Uploaded lecorguille parents: diff changeset	79
17 95e689b7f27f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 878be1bfbe93af0a140df76fa47f0a82a48189e3 lecorguille parents: 14 diff changeset	80 <expand macro="input_peaklist_conditional"/>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	81
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	82 <expand macro="input_file_load"/>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	83 </inputs>
f3f97841564f Uploaded lecorguille parents: diff changeset	84
f3f97841564f Uploaded lecorguille parents: diff changeset	85 <outputs>
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	86 <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	87 <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	88 <expand macro="output_peaklist" function="group"/>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	89 </outputs>
f3f97841564f Uploaded lecorguille parents: diff changeset	90
f3f97841564f Uploaded lecorguille parents: diff changeset	91 <tests>
27 d45a786cbc40 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 26 diff changeset	92 <!-- from merge -->
d45a786cbc40 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 26 diff changeset	93 <!-- DISABLE FOR TRAVIS but useful in order to REFRESH TEST-DATA
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	94 <test>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	95 <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	96 <conditional name="methods">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	97 <param name="method" value="PeakDensity"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	98 <param name="bw" value="5"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	99 <param name="minFraction" value="0.3"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	100 <param name="binSize" value="0.01"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	101 <section name="PeakDensityAdv">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	102 <param name="maxFeatures" value="50"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	103 </section>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	104 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	105 <conditional name="peaklist">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	106 <param name="peaklistBool" value="true" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	107 <param name="convertRTMinute" value="false" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	108 <param name="numDigitsMZ" value="4" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	109 <param name="numDigitsRT" value="1" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	110 <param name="naTOzero" value="false" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	111 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	112 <expand macro="test_file_load_single"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	113 <assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	114 <has_text text="bw: 5" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	115 <has_text text="minFraction: 0.3" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	116 <has_text text="maxFeatures: 50" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	117 <has_text text="object with 4 samples" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	118 <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	119 <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	120 <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	121 <has_text text="Peak Groups: 8372" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	122 <has_text text="Sample classes: KO, WT" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	123 </assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	124 <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	125 <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	126 </test>-->
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	127 <!-- DISABLE FOR TRAVIS
5 0306a96cc446 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	128 <test>
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	129 <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	130 <conditional name="methods">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	131 <param name="method" value="PeakDensity"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	132 <param name="bw" value="5"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	133 <param name="minFraction" value="0.3"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	134 <param name="binSize" value="0.01"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	135 <conditional name="density_options">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	136 <param name="option" value="show"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	137 <param name="maxFeatures" value="50"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	138 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	139 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	140 <expand macro="test_file_load_single"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	141 <assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	142 <has_text text="object with 4 samples" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	143 <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	144 <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	145 <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	146 <has_text text="Peak Groups: 611" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	147 <has_text text="Sample classes: ." />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	148 </assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	149 </test>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	150 -->
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	151 <!-- DISABLE FOR TRAVIS Zip from xcmsSet
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	152 <test>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	153 <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	154 <conditional name="methods">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	155 <param name="method" value="PeakDensity"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	156 <param name="bw" value="5"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	157 <param name="minFraction" value="0.3"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	158 <param name="binSize" value="0.01"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	159 <conditional name="density_options">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	160 <param name="option" value="show"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	161 <param name="maxFeatures" value="50"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	162 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	163 </conditional>
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	164 <conditional name="peaklist">
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	165 <param name="convertRTMinute" value="false" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	166 <param name="peaklistBool" value="true" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	167 <param name="numDigitsMZ" value="4" />
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	168 <param name="numDigitsRT" value="1" />
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	169 <param name="naTOzero" value="false" />
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	170 </conditional>
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	171 <expand macro="test_file_load_zip"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	172 <assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	173 <has_text text="object with 4 samples" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	174 <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	175 <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	176 <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	177 <has_text text="Peak Groups: 8372" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	178 <has_text text="Sample classes: KO, WT" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	179 </assert_stdout>
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	180 <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	181 <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	182 </test>
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	183 -->
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	184
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	185 <!-- DISABLE FOR TRAVIS Zip from retcor
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	186 <test>
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	187 <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	188 <conditional name="methods">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	189 <param name="method" value="PeakDensity"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	190 <param name="bw" value="5"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	191 <param name="minFraction" value="0.3"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	192 <param name="binSize" value="0.01"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	193 <conditional name="density_options">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	194 <param name="option" value="show"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	195 <param name="maxFeatures" value="50"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	196 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	197 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	198 <expand macro="test_file_load_zip"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	199 <assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	200 <has_text text="object with 4 samples" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	201 <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	202 <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	203 <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	204 <has_text text="Peak Groups: 8209" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	205 <has_text text="Sample classes: KO, WT" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	206 </assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	207 </test>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	208 -->
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	209 <!-- from retcor -->
28 2b676d5eb848 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e workflow4metabolomics parents: 27 diff changeset	210 <test expect_num_outputs="4">
27 d45a786cbc40 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 26 diff changeset	211 <param name="image" value="faahKO-single-class.xset.merged.group.retcor.RData" ftype="rdata"/>
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	212 <conditional name="methods">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	213 <param name="method" value="PeakDensity"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	214 <param name="bw" value="5"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	215 <param name="minFraction" value="0.3"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	216 <param name="binSize" value="0.01"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	217 <section name="PeakDensityAdv">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	218 <param name="maxFeatures" value="50"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	219 </section>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	220 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	221 <expand macro="test_file_load_single"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	222 <assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	223 <has_text text="bw: 5" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	224 <has_text text="minFraction: 0.3" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	225 <has_text text="binSize: 0.01"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	226 <has_text text="maxFeatures: 50" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	227 <has_text text="object with 4 samples" />
27 d45a786cbc40 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 26 diff changeset	228 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	229 <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	230 <has_text text="Peaks: 9251 (about 2313 per sample)" />
27 d45a786cbc40 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 26 diff changeset	231 <has_text text="Peak Groups: 8209" />
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	232 <has_text text="Sample classes: KO, WT" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	233 </assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	234 </test>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	235 <!-- DISABLE FOR TRAVIS
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	236 Test to test the different methods parameters
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	237 <test expect_failure="True">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	238 <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	239 <conditional name="methods">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	240 <param name="method" value="MzClust"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	241 <param name="ppm" value="21"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	242 <param name="absMz" value="0.1"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	243 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	244 <expand macro="test_file_load_single"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	245 <assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	246 <has_text text="ppm: 21" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	247 <has_text text="absMz: 0.1" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	248 </assert_stdout>
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	249 </test>
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	250 <test>
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	251 <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	252 <conditional name="methods">
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	253 <param name="method" value="NearestPeaks"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	254 <param name="mzVsRtBalance" value="11"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	255 <param name="absMz" value="0.1"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	256 </conditional>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	257 <expand macro="test_file_load_single"/>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	258 <assert_stdout>
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	259 <has_text text="mzVsRtBalance: 11" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	260 <has_text text="absMz: 0.1" />
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	261 </assert_stdout>
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	262 </test>
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	263 -->
0 f3f97841564f Uploaded lecorguille parents: diff changeset	264 </tests>
f3f97841564f Uploaded lecorguille parents: diff changeset	265
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	266 <help><![CDATA[
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	267
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	268 @HELP_AUTHORS@
0 f3f97841564f Uploaded lecorguille parents: diff changeset	269
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	270 ====================
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	271 xcms groupChromPeaks
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	272 ====================
0 f3f97841564f Uploaded lecorguille parents: diff changeset	273
f3f97841564f Uploaded lecorguille parents: diff changeset	274 -----------
f3f97841564f Uploaded lecorguille parents: diff changeset	275 Description
f3f97841564f Uploaded lecorguille parents: diff changeset	276 -----------
f3f97841564f Uploaded lecorguille parents: diff changeset	277
f3f97841564f Uploaded lecorguille parents: diff changeset	278 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	279
f3f97841564f Uploaded lecorguille parents: diff changeset	280 -----------------
f3f97841564f Uploaded lecorguille parents: diff changeset	281 Workflow position
f3f97841564f Uploaded lecorguille parents: diff changeset	282 -----------------
f3f97841564f Uploaded lecorguille parents: diff changeset	283
f3f97841564f Uploaded lecorguille parents: diff changeset	284 Upstream tools
f3f97841564f Uploaded lecorguille parents: diff changeset	285
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	286 ==================================== ======================== ==============================
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	287 Name Output file Format
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	288 ==================================== ======================== ==============================
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	289 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	290 ------------------------------------ ------------------------ ------------------------------
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	291 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	292 ------------------------------------ ------------------------ ------------------------------
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	293 xcms.adjustRtime ``*``.adjustRtime.RData rdata.xcms.retcor
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	294 ==================================== ======================== ==============================
0 f3f97841564f Uploaded lecorguille parents: diff changeset	295
f3f97841564f Uploaded lecorguille parents: diff changeset	296
f3f97841564f Uploaded lecorguille parents: diff changeset	297 Downstream tools
f3f97841564f Uploaded lecorguille parents: diff changeset	298
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	299 =========================== =========================== ====================
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	300 Name Output file Format
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	301 =========================== =========================== ====================
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	302 xcms.adjustRtime ``*``.groupChromPeaks.RData rdata.xcms.group
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	303 --------------------------- --------------------------- --------------------
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	304 xcms.fillChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	305 =========================== =========================== ====================
0 f3f97841564f Uploaded lecorguille parents: diff changeset	306
f3f97841564f Uploaded lecorguille parents: diff changeset	307 General schema of the metabolomic workflow
f3f97841564f Uploaded lecorguille parents: diff changeset	308
f3f97841564f Uploaded lecorguille parents: diff changeset	309 .. image:: xcms_group_workflow.png
f3f97841564f Uploaded lecorguille parents: diff changeset	310
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	311 ---------------------------------------------------
0 f3f97841564f Uploaded lecorguille parents: diff changeset	312
f3f97841564f Uploaded lecorguille parents: diff changeset	313 ----------
f3f97841564f Uploaded lecorguille parents: diff changeset	314 Parameters
f3f97841564f Uploaded lecorguille parents: diff changeset	315 ----------
f3f97841564f Uploaded lecorguille parents: diff changeset	316
f3f97841564f Uploaded lecorguille parents: diff changeset	317 Method to use for grouping
f3f97841564f Uploaded lecorguille parents: diff changeset	318 --------------------------
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 MzClust
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	321
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	322 \| 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	323 \| See the MzClust_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 PeakDensity
0 f3f97841564f Uploaded lecorguille parents: diff changeset	326
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	327 \| 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	328 \| See the PeakDensity_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 NearestPeaks
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	331
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	332 \| 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	333 \| See the NearestPeaks_manual_
0 f3f97841564f Uploaded lecorguille parents: diff changeset	334
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	335 .. _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	336 .. _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	337 .. _NearestPeaks_manual: https://rdrr.io/bioc/xcms/man/groupChromPeaks-nearest.html#heading-2
0 f3f97841564f Uploaded lecorguille parents: diff changeset	338
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	339 @HELP_XCMS_MANUAL@
0 f3f97841564f Uploaded lecorguille parents: diff changeset	340
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	341 @HELP_PEAKLIST@
0 f3f97841564f Uploaded lecorguille parents: diff changeset	342
f3f97841564f Uploaded lecorguille parents: diff changeset	343 ------------
f3f97841564f Uploaded lecorguille parents: diff changeset	344 Output files
f3f97841564f Uploaded lecorguille parents: diff changeset	345 ------------
f3f97841564f Uploaded lecorguille parents: diff changeset	346
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	347 xset.groupChromPeaks.RData: rdata.xcms.group format
0 f3f97841564f Uploaded lecorguille parents: diff changeset	348
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	349 \| 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	350
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	351 xset.groupChromPeaks.plotChromPeakDensity.pdf
0 f3f97841564f Uploaded lecorguille parents: diff changeset	352
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	353 \| Density plot
0 f3f97841564f Uploaded lecorguille parents: diff changeset	354
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	355 @HELP_PEAKLIST_OUTPUT@
0 f3f97841564f Uploaded lecorguille parents: diff changeset	356
f3f97841564f Uploaded lecorguille parents: diff changeset	357
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	358 ---------------------------------------------------
2 ed149026836e Uploaded mmonsoor parents: 0 diff changeset	359
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	360 Changelog/News
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	361 --------------
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	362
27 d45a786cbc40 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae" workflow4metabolomics parents: 26 diff changeset	363 @HELP_XCMS_NEWVERSION_31200@
19 c8f8d598f562 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639 lecorguille parents: 18 diff changeset	364
25 a066b8581b97 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40" workflow4metabolomics parents: 24 diff changeset	365 Version 3.6.1+galaxy1 - 22/04/2020
a066b8581b97 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40" workflow4metabolomics parents: 24 diff changeset	366
a066b8581b97 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40" workflow4metabolomics parents: 24 diff changeset	367 - BUGFIX: sample group colours were not displayed in plots.
a066b8581b97 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40" workflow4metabolomics parents: 24 diff changeset	368
24 761913919c21 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 20 diff changeset	369 @HELP_XCMS_NEWVERSION_3610@
20 63d9c5980c07 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d481a27556155e3587901d702d364b71f28e30b9 lecorguille parents: 19 diff changeset	370
24 761913919c21 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617" workflow4metabolomics parents: 20 diff changeset	371 @HELP_XCMS_NEWVERSION_3440@
19 c8f8d598f562 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639 lecorguille parents: 18 diff changeset	372
c8f8d598f562 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639 lecorguille parents: 18 diff changeset	373 - 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	374
c8f8d598f562 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639 lecorguille parents: 18 diff changeset	375 - 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	376
18 7a19925478e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 lecorguille parents: 17 diff changeset	377 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	378
7a19925478e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989 lecorguille parents: 17 diff changeset	379 - 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	380
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	381 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	382
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	383 - 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	384
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	385 - 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	386
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	387 - NEW: a new density plot
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	388
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	389 - 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	390
833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	391
13 13558e8a4778 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	392 Version 2.1.1 - 29/11/2017
13558e8a4778 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	393
13558e8a4778 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	394 - 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	395
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	396
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	397 Version 2.1.0 - 07/02/2017
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	398
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	399 - 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	400
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	401 - 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	402
c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	403 - 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	404
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	405
8 5d80e7511dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 5 diff changeset	406 Version 2.0.6 - 06/07/2016
5d80e7511dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 5 diff changeset	407
5d80e7511dfb planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 5 diff changeset	408 - 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	409
14 833d2c821d9c planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857 lecorguille parents: 13 diff changeset	410
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	411 Version 2.0.5 - 04/04/2016
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	412
10 c81275aee959 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 8 diff changeset	413 - 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	414
2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	415
3 98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	416 Version 2.0.4 - 10/02/2016
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	417
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	418 - BUGFIX: better management of errors. Datasets remained green although the process failed
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	419
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	420 - UPDATE: refactoring of internal management of inputs/outputs
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	421
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	422 - UPDATE: refactoring to feed the new report tool
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	423
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	424
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	425 Version 2.0.2 - 02/06/2015
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	426
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	427 - 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	428
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	429 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	430
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	431
98e33cdf0eb1 planemo upload lecorguille parents: 2 diff changeset	432 ]]></help>
0 f3f97841564f Uploaded lecorguille parents: diff changeset	433
f3f97841564f Uploaded lecorguille parents: diff changeset	434
4 2db1d1d0f131 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 3 diff changeset	435 <expand macro="citation" />
0 f3f97841564f Uploaded lecorguille parents: diff changeset	436
f3f97841564f Uploaded lecorguille parents: diff changeset	437
f3f97841564f Uploaded lecorguille parents: diff changeset	438 </tool>

Mercurial > repos > lecorguille > xcms_group

annotate abims_xcms_group.xml @ 30:3820e3f3b1cb draft default tip