xcms_group: abims_xcms_group.xml annotate

annotate abims_xcms_group.xml @ 31:f248fd3b89d6 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309

author	lecorguille
date	Thu, 08 Mar 2018 05:53:40 -0500
parents	020d065edd9e
children	68282292acc4

rev	line source
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	1 <tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@WRAPPER_VERSION@.0">
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	2
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	3 <description>Perform the correspondence, the grouping of chromatographic peaks within and between samples.</description>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	4
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	5 <macros>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	6 <import>macros.xml</import>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	7 </macros>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	8
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	9 <expand macro="requirements"/>
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	10 <expand macro="stdio"/>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	11
1 df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	12 <command><![CDATA[
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	13 @COMMAND_XCMS_SCRIPT@/xcms_group.r
19 7f667b64d5a5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4 lecorguille parents: 17 diff changeset	14 image '$image'
1 df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	15
27 36b470f3ebcf planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 26 diff changeset	16 method $methods.method
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	17 #if $methods.method == "PeakDensity":
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	18 bw $methods.bw
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	19 minFraction $methods.minFraction
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	20 minSamples $methods.minSamples
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	21 binSize $methods.binSize
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	22 ## Advanced
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	23 maxFeatures $methods.PeakDensityAdv.maxFeatures
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	24 #elif $methods.method == "MzClust":
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	25 ppm $methods.ppm
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	26 absMz $methods.absMz
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	27 minFraction $methods.minFraction
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	28 minSamples $methods.minSamples
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	29 #else:
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	30 mzVsRtBalance $methods.mzVsRtBalance
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	31 absMz $methods.absMz
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	32 absRt $methods.absRt
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	33 kNN $methods.kNN
2a104ea58d12 Uploaded lecorguille parents: diff changeset	34 #end if
17 a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	35
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	36 @COMMAND_PEAKLIST@
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	37
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	38 @COMMAND_FILE_LOAD@
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	39
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	40 @COMMAND_LOG_EXIT@
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	41 ]]></command>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	42
2a104ea58d12 Uploaded lecorguille parents: diff changeset	43 <inputs>
31 f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 29 diff changeset	44 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks or adjustRtime" />
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	45 <conditional name="methods">
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	46 <param name="method" type="select" label="Method to use for grouping" help="See the help section below">
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	47 <option value="PeakDensity" selected="true">PeakDensity - peak grouping based on time dimension peak densities</option>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	48 <option value="MzClust">MzClust - high resolution peak grouping for single spectra (direct infusion) MS data</option>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	49 <option value="NearestPeaks">NearestPeaks - chromatographic peak grouping based on their proximity in the mz-rt space</option>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	50 </param>
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	51 <when value="PeakDensity">
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	52 <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" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	53 <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)" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	54 <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)" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	55 <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)" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	56
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	57 <section name="PeakDensityAdv" title="Advanced Options" expanded="False">
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	58 <param argument="maxFeatures" type="integer" value="50" label="Maximum number of groups to identify in a single m/z slice" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	59 </section>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	60 </when>
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	61 <when value="MzClust">
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	62 <param argument="ppm" type="integer" value="20" label="Relative mz error for clustering/grouping in ppm" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	63 <param argument="absMz" type="float" value="0" label="Absolute mz error for clustering/grouping" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	64 <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)" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	65 <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)" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	66 </when>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	67 <when value="NearestPeaks">
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	68 <param argument="mzVsRtBalance" type="integer" value="10" label="Factor by which mz values are multiplied before calculating the (euclician) distance between two peaks" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	69 <param argument="absMz" type="float" value="0.2" label="Maximum tolerated distance for mz values" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	70 <param argument="absRt" type="integer" value="15" label="Maximum tolerated distance for RT values" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	71 <param argument="kNN" type="integer" value="10" label="Number of nearest Neighbours to check" />
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	72 </when>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	73 </conditional>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	74
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	75 <expand macro="input_peaklist"/>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	76
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	77 <expand macro="input_file_load"/>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	78 </inputs>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	79
2a104ea58d12 Uploaded lecorguille parents: diff changeset	80 <outputs>
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	81 <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData" from_work_dir="group.RData"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	82 <data name="plotChromPeakDensity" format="pdf" label="${image.name[:-6]}.group.plotChromPeakDensity.pdf" from_work_dir="plotChromPeakDensity.pdf"/>
24 1a7d1f9e8912 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b8ea02b3d37550c33dcf8e099fe8c636287b0865 lecorguille parents: 22 diff changeset	83 <expand macro="output_peaklist" function="group"/>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	84 </outputs>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	85
2a104ea58d12 Uploaded lecorguille parents: diff changeset	86 <tests>
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	87 <!-- from xcmsSet -->
7 75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	88 <test>
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	89 <param name="image" value="faahKO-single-class.xset.merged.RData"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	90 <conditional name="methods">
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	91 <param name="method" value="PeakDensity"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	92 <param name="bw" value="5"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	93 <param name="minFraction" value="0.3"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	94 <param name="binSize" value="0.01"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	95 <section name="PeakDensityAdv">
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	96 <param name="maxFeatures" value="50"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	97 </section>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	98 </conditional>
17 a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	99 <conditional name="peaklist">
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	100 <param name="peaklistBool" value="true" />
17 a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	101 <param name="convertRTMinute" value="false" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	102 <param name="numDigitsMZ" value="4" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	103 <param name="numDigitsRT" value="1" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	104 </conditional>
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	105 <expand macro="test_file_load_single"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	106 <assert_stdout>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	107 <has_text text="bw: 5" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	108 <has_text text="minFraction: 0.3" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	109 <has_text text="maxFeatures: 50" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	110 <has_text text="object with 4 samples" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	111 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	112 <has_text text="Mass range: 200.1-600 m/z" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	113 <has_text text="Peaks: 9251 (about 2313 per sample)" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	114 <has_text text="Peak Groups: 8372" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	115 <has_text text="Sample classes: KO, WT" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	116 </assert_stdout>
17 a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	117 <output name="variableMetadata" file="faahKO.xset.group.variableMetadata.tsv" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	118 <output name="dataMatrix" file="faahKO.xset.group.dataMatrix.tsv" />
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	119 </test>
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	120 <!-- DISABLE FOR TRAVIS
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	121 <test>
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	122 <param name="image" value="faahKO-single.xset.merged.RData"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	123 <conditional name="methods">
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	124 <param name="method" value="PeakDensity"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	125 <param name="bw" value="5"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	126 <param name="minFraction" value="0.3"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	127 <param name="binSize" value="0.01"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	128 <conditional name="density_options">
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	129 <param name="option" value="show"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	130 <param name="maxFeatures" value="50"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	131 </conditional>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	132 </conditional>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	133 <expand macro="test_file_load_single"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	134 <assert_stdout>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	135 <has_text text="object with 4 samples" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	136 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	137 <has_text text="Mass range: 200.1-600 m/z" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	138 <has_text text="Peaks: 9251 (about 2313 per sample)" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	139 <has_text text="Peak Groups: 611" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	140 <has_text text="Sample classes: ." />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	141 </assert_stdout>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	142 </test>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	143 -->
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	144 <!-- DISABLE FOR TRAVIS Zip from xcmsSet
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	145 <test>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	146 <param name="image" value="faahKO.xset.RData"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	147 <conditional name="methods">
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	148 <param name="method" value="PeakDensity"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	149 <param name="bw" value="5"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	150 <param name="minFraction" value="0.3"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	151 <param name="binSize" value="0.01"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	152 <conditional name="density_options">
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	153 <param name="option" value="show"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	154 <param name="maxFeatures" value="50"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	155 </conditional>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	156 </conditional>
17 a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	157 <conditional name="peaklist">
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	158 <param name="convertRTMinute" value="false" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	159 <param name="peaklistBool" value="true" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	160 <param name="numDigitsMZ" value="4" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	161 <param name="numDigitsRT" value="1" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	162 </conditional>
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	163 <expand macro="test_file_load_zip"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	164 <assert_stdout>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	165 <has_text text="object with 4 samples" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	166 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	167 <has_text text="Mass range: 200.1-600 m/z" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	168 <has_text text="Peaks: 9251 (about 2313 per sample)" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	169 <has_text text="Peak Groups: 8372" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	170 <has_text text="Sample classes: KO, WT" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	171 </assert_stdout>
17 a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	172 <output name="variableMetadata" file="faahKO.xset.group.variableMetadata.tsv" />
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	173 <output name="dataMatrix" file="faahKO.xset.group.dataMatrix.tsv" />
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	174 </test>
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	175 -->
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	176
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	177 <!-- DISABLE FOR TRAVIS Zip from retcor
7 75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	178 <test>
75be85d996d9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 4 diff changeset	179 <param name="image" value="faahKO.xset.group.retcor.RData"/>
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	180 <conditional name="methods">
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	181 <param name="method" value="PeakDensity"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	182 <param name="bw" value="5"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	183 <param name="minFraction" value="0.3"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	184 <param name="binSize" value="0.01"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	185 <conditional name="density_options">
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	186 <param name="option" value="show"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	187 <param name="maxFeatures" value="50"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	188 </conditional>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	189 </conditional>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	190 <expand macro="test_file_load_zip"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	191 <assert_stdout>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	192 <has_text text="object with 4 samples" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	193 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	194 <has_text text="Mass range: 200.1-600 m/z" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	195 <has_text text="Peaks: 9251 (about 2313 per sample)" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	196 <has_text text="Peak Groups: 8209" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	197 <has_text text="Sample classes: KO, WT" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	198 </assert_stdout>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	199 </test>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	200 -->
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	201 <!-- from retcor -->
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	202 <test>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	203 <param name="image" value="faahKO-single.xset.merged.group.retcor.RData"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	204 <conditional name="methods">
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	205 <param name="method" value="PeakDensity"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	206 <param name="bw" value="5"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	207 <param name="minFraction" value="0.3"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	208 <param name="binSize" value="0.01"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	209 <section name="PeakDensityAdv">
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	210 <param name="maxFeatures" value="50"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	211 </section>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	212 </conditional>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	213 <expand macro="test_file_load_single"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	214 <assert_stdout>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	215 <has_text text="bw: 5" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	216 <has_text text="minFraction: 0.3" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	217 <has_text text="binSize: 0.01"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	218 <has_text text="maxFeatures: 50" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	219 <has_text text="object with 4 samples" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	220 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	221 <has_text text="Mass range: 200.1-600 m/z" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	222 <has_text text="Peaks: 9251 (about 2313 per sample)" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	223 <has_text text="Peak Groups: 8209" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	224 <has_text text="Sample classes: KO, WT" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	225 </assert_stdout>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	226 </test>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	227 <!-- DISABLE FOR TRAVIS
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	228 Test to test the different methods parameters
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	229 <test expect_failure="True">
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	230 <param name="image" value="faahKO-single.xset.merged.group.retcor.RData"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	231 <conditional name="methods">
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	232 <param name="method" value="MzClust"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	233 <param name="ppm" value="21"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	234 <param name="absMz" value="0.1"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	235 </conditional>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	236 <expand macro="test_file_load_single"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	237 <assert_stdout>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	238 <has_text text="ppm: 21" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	239 <has_text text="absMz: 0.1" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	240 </assert_stdout>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	241 </test>
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	242 <test>
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	243 <param name="image" value="faahKO-single.xset.merged.group.retcor.RData"/>
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	244 <conditional name="methods">
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	245 <param name="method" value="NearestPeaks"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	246 <param name="mzVsRtBalance" value="11"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	247 <param name="absMz" value="0.1"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	248 </conditional>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	249 <expand macro="test_file_load_single"/>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	250 <assert_stdout>
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	251 <has_text text="mzVsRtBalance: 11" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	252 <has_text text="absMz: 0.1" />
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	253 </assert_stdout>
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	254 </test>
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	255 -->
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	256 </tests>
2a104ea58d12 Uploaded lecorguille parents: diff changeset	257
1 df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	258 <help><![CDATA[
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	259
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	260 @HELP_AUTHORS@
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	261
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	262 ====================
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	263 xcms groupChromPeaks
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	264 ====================
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	265
28 a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	266 -----------
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	267 Description
2a104ea58d12 Uploaded lecorguille parents: diff changeset	268 -----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	269
2a104ea58d12 Uploaded lecorguille parents: diff changeset	270 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.
2a104ea58d12 Uploaded lecorguille parents: diff changeset	271
28 a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	272 -----------------
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	273 Workflow position
2a104ea58d12 Uploaded lecorguille parents: diff changeset	274 -----------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	275
2a104ea58d12 Uploaded lecorguille parents: diff changeset	276 Upstream tools
2a104ea58d12 Uploaded lecorguille parents: diff changeset	277
28 a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	278 ========================= ================= =================== ==========
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	279 Name output file format parameter
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	280 ========================= ================= =================== ==========
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	281 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	282 ------------------------- ----------------- ------------------- ----------
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	283 xcms.xcmsSet Merger xset.RData rdata.xcms.raw RData file
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	284 ------------------------- ----------------- ------------------- ----------
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	285 xcms.retcor xset.RData rdata.xcms.retcor RData file
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	286 ========================= ================= =================== ==========
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	287
2a104ea58d12 Uploaded lecorguille parents: diff changeset	288
2a104ea58d12 Uploaded lecorguille parents: diff changeset	289 Downstream tools
2a104ea58d12 Uploaded lecorguille parents: diff changeset	290
2a104ea58d12 Uploaded lecorguille parents: diff changeset	291 +---------------------------+--------------------------------------+
2a104ea58d12 Uploaded lecorguille parents: diff changeset	292 \| Name \| Output file \| Format \|
2a104ea58d12 Uploaded lecorguille parents: diff changeset	293 +===========================+=================+====================+
2a104ea58d12 Uploaded lecorguille parents: diff changeset	294 \|xcms.retcor \| xset.RData \| rdata.xcms.group \|
2a104ea58d12 Uploaded lecorguille parents: diff changeset	295 +---------------------------+--------------------------------------+
2a104ea58d12 Uploaded lecorguille parents: diff changeset	296 \|xcms.fillPeaks \| xset.RData \| rdata.xcms.group \|
2a104ea58d12 Uploaded lecorguille parents: diff changeset	297 +---------------------------+--------------------------------------+
2a104ea58d12 Uploaded lecorguille parents: diff changeset	298
28 a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	299 The output file is an xcmsSet.RData file. You can continue your analysis using it in xcms.retcor tool as an next step and then xcms.fillPeaks.
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	300
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	301 General schema of the metabolomic workflow
2a104ea58d12 Uploaded lecorguille parents: diff changeset	302
2a104ea58d12 Uploaded lecorguille parents: diff changeset	303 .. image:: xcms_group_workflow.png
2a104ea58d12 Uploaded lecorguille parents: diff changeset	304
2a104ea58d12 Uploaded lecorguille parents: diff changeset	305
2a104ea58d12 Uploaded lecorguille parents: diff changeset	306 -----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	307 Input files
2a104ea58d12 Uploaded lecorguille parents: diff changeset	308 -----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	309
2a104ea58d12 Uploaded lecorguille parents: diff changeset	310 +---------------------------+-----------------------+
28 a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	311 \| Parameter : num + label \| Format \|
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	312 +===========================+=======================+
28 a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	313 \| Or : RData file \| rdata.xcms.raw \|
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	314 +---------------------------+-----------------------+
28 a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	315 \| Or : RData file \| rdata.xcms.retcor \|
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	316 +---------------------------+-----------------------+
2a104ea58d12 Uploaded lecorguille parents: diff changeset	317
2a104ea58d12 Uploaded lecorguille parents: diff changeset	318
2a104ea58d12 Uploaded lecorguille parents: diff changeset	319 ----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	320 Parameters
2a104ea58d12 Uploaded lecorguille parents: diff changeset	321 ----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	322
2a104ea58d12 Uploaded lecorguille parents: diff changeset	323 Method to use for grouping
2a104ea58d12 Uploaded lecorguille parents: diff changeset	324 --------------------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	325
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	326 MzClust
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	327
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	328 \| This method performs high resolution correspondence for single spectra samples.
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	329 \| See the MzClust_manual_
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	330
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	331 PeakDensity
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	332
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	333 \| 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).
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	334 \| See the PeakDensity_manual_
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	335
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	336 NearestPeaks
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	337
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	338 \| 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.
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	339 \| See the NearestPeaks_manual_
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	340
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	341 .. _MzClust_manual: https://rdrr.io/bioc/xcms/man/groupChromPeaks-mzClust.html#heading-2
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	342 .. _PeakDensity_manual: https://rdrr.io/bioc/xcms/man/groupChromPeaks-density.html#heading-2
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	343 .. _NearestPeaks_manual: https://rdrr.io/bioc/xcms/man/groupChromPeaks-nearest.html#heading-2
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	344
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	345 @HELP_XCMS_MANUAL@
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	346
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	347 @HELP_PEAKLIST@
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	348
2a104ea58d12 Uploaded lecorguille parents: diff changeset	349 ------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	350 Output files
2a104ea58d12 Uploaded lecorguille parents: diff changeset	351 ------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	352
28 a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	353 xset.group.Rplots.pdf
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	354
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	355 xset.group.RData: rdata.xcms.group format
2a104ea58d12 Uploaded lecorguille parents: diff changeset	356
2a104ea58d12 Uploaded lecorguille parents: diff changeset	357 \| Rdata file that will be necessary in the third and fourth step of the workflow (xcms.retcor and xcms.fillpeaks).
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	358
28 a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	359
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	360 ------
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	361
28 a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	362 .. class:: infomark
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	363
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	364 The output file is an xset.group.RData file. You can continue your analysis using it in xcms.retcor tool.
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	365
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	366
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	367 ---------------------------------------------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	368
2a104ea58d12 Uploaded lecorguille parents: diff changeset	369
2a104ea58d12 Uploaded lecorguille parents: diff changeset	370 ---------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	371 Working example
2a104ea58d12 Uploaded lecorguille parents: diff changeset	372 ---------------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	373
2a104ea58d12 Uploaded lecorguille parents: diff changeset	374 Input files
2a104ea58d12 Uploaded lecorguille parents: diff changeset	375 -----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	376
2a104ea58d12 Uploaded lecorguille parents: diff changeset	377 \| RData file -> xset.RData
2a104ea58d12 Uploaded lecorguille parents: diff changeset	378
2a104ea58d12 Uploaded lecorguille parents: diff changeset	379 Parameters
2a104ea58d12 Uploaded lecorguille parents: diff changeset	380 ----------
2a104ea58d12 Uploaded lecorguille parents: diff changeset	381
28 a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	382 \| Method -> density
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	383 \| bw -> 5
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	384 \| minFraction -> 0.3
020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	385 \| binSize -> 0.01
28 a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	386 \| Advanced options: show
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	387 \| maxFeatures -> 50
28 a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	388
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	389
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	390 Output files
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	391 ------------
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	392
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	393 \| 1) xset.RData: RData file
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	394
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	395 \| 2) Example of an xset.group.Rplots pdf file
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	396
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	397 .. image:: xcms_group.png
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	398 :width: 700
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	399
2a104ea58d12 Uploaded lecorguille parents: diff changeset	400
3 003373d58672 planemo upload lecorguille parents: 2 diff changeset	401 ---------------------------------------------------
003373d58672 planemo upload lecorguille parents: 2 diff changeset	402
003373d58672 planemo upload lecorguille parents: 2 diff changeset	403 Changelog/News
003373d58672 planemo upload lecorguille parents: 2 diff changeset	404 --------------
31 f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 29 diff changeset	405
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 29 diff changeset	406 Version 3.0.0.0 - 08/03/2018
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 29 diff changeset	407
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 29 diff changeset	408 - 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.
29 020d065edd9e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: 28 diff changeset	409
31 f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 29 diff changeset	410 - NEW: a bunch of new options: PeakDensity.minSamples), MzClust.minSamples)
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 29 diff changeset	411
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 29 diff changeset	412 - NEW: a new density plot
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 29 diff changeset	413
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 29 diff changeset	414 - IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values.
f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 29 diff changeset	415
3 003373d58672 planemo upload lecorguille parents: 2 diff changeset	416
28 a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	417 Version 2.1.1 - 29/11/2017
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	418
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	419 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
a18fc7554c6d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298 lecorguille parents: 27 diff changeset	420
31 f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 29 diff changeset	421
19 7f667b64d5a5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4 lecorguille parents: 17 diff changeset	422 Version 2.1.0 - 07/02/2017
17 a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	423
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	424 - IMPROVEMENT: Add an option to export the peak list at this step without have to wait camara.annotate
a28473761624 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty lecorguille parents: 16 diff changeset	425
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	426 - IMPROVEMENT: xcms.group can deal with merged individual data from "xcms.xcmsSet Merger"
f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	427
22 b41669de74ae planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 19 diff changeset	428 - 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
b41669de74ae planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 19 diff changeset	429
31 f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 29 diff changeset	430
10 676c748b23ea planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 7 diff changeset	431 Version 2.0.6 - 06/07/2016
676c748b23ea planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 7 diff changeset	432
676c748b23ea planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 7 diff changeset	433 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
676c748b23ea planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 7 diff changeset	434
31 f248fd3b89d6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 29 diff changeset	435
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	436 Version 2.0.5 - 04/04/2016
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	437
14 f4dc089f9d19 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 10 diff changeset	438 - TEST: refactoring to pass planemo test using conda dependencies
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	439
fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	440
3 003373d58672 planemo upload lecorguille parents: 2 diff changeset	441 Version 2.0.4 - 10/02/2016
003373d58672 planemo upload lecorguille parents: 2 diff changeset	442
003373d58672 planemo upload lecorguille parents: 2 diff changeset	443 - BUGFIX: better management of errors. Datasets remained green although the process failed
003373d58672 planemo upload lecorguille parents: 2 diff changeset	444
003373d58672 planemo upload lecorguille parents: 2 diff changeset	445 - UPDATE: refactoring of internal management of inputs/outputs
003373d58672 planemo upload lecorguille parents: 2 diff changeset	446
003373d58672 planemo upload lecorguille parents: 2 diff changeset	447 - UPDATE: refactoring to feed the new report tool
003373d58672 planemo upload lecorguille parents: 2 diff changeset	448
003373d58672 planemo upload lecorguille parents: 2 diff changeset	449
003373d58672 planemo upload lecorguille parents: 2 diff changeset	450 Version 2.0.2 - 02/06/2015
003373d58672 planemo upload lecorguille parents: 2 diff changeset	451
003373d58672 planemo upload lecorguille parents: 2 diff changeset	452 - 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.
003373d58672 planemo upload lecorguille parents: 2 diff changeset	453
003373d58672 planemo upload lecorguille parents: 2 diff changeset	454 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
003373d58672 planemo upload lecorguille parents: 2 diff changeset	455
003373d58672 planemo upload lecorguille parents: 2 diff changeset	456
1 df264428a5e1 Uploaded lecorguille parents: 0 diff changeset	457 ]]></help>
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	458
2a104ea58d12 Uploaded lecorguille parents: diff changeset	459
4 fef3d1b8e7f4 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 3 diff changeset	460 <expand macro="citation" />
0 2a104ea58d12 Uploaded lecorguille parents: diff changeset	461
2a104ea58d12 Uploaded lecorguille parents: diff changeset	462
2a104ea58d12 Uploaded lecorguille parents: diff changeset	463 </tool>

Mercurial > repos > lecorguille > xcms_group

annotate abims_xcms_group.xml @ 31:f248fd3b89d6 draft