xcms_xcmsset: abims_xcms_xcmsSet.xml annotate

annotate abims_xcms_xcmsSet.xml @ 13:c934dd5c49a9 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1

author	lecorguille
date	Wed, 29 Nov 2017 09:45:19 -0500
parents	15646e937936
children	b62808a2a008

rev	line source
13 c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	1 <tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.1.1">
0 054e4681667c planemo upload lecorguille parents: diff changeset	2 <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	3
6 0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	4 <macros>
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	5 <import>macros.xml</import>
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	6 </macros>
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	7
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	8 <expand macro="requirements"/>
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	9 <expand macro="stdio"/>
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	10
5 588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	11 <command><![CDATA[
6 0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	12 @COMMAND_XCMS_SCRIPT@
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	13
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	14 #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"):
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	15 singlefile_galaxyPath '$input' singlefile_sampleName '$input.name'
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	16 #else
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	17 zipfile '$input'
0 054e4681667c planemo upload lecorguille parents: diff changeset	18 #end if
054e4681667c planemo upload lecorguille parents: diff changeset	19
054e4681667c planemo upload lecorguille parents: diff changeset	20 xfunction xcmsSet
5 588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	21
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	22 xsetRdataOutput '$xsetRData'
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	23 sampleMetadataOutput '$sampleMetadata'
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	24 ticspdf '$ticsRawPdf'
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	25 bicspdf '$bpcsRawPdf'
5 588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	26
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	27
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	28 #if $options_scanrange.option == "show":
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	29 scanrange "c($options_scanrange.scanrange)"
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	30 #end if
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	31
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	32 ## profmethod $profmethod
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	33 nSlaves \${GALAXY_SLOTS:-1} method $methods.method
0 054e4681667c planemo upload lecorguille parents: diff changeset	34 #if $methods.method == "centWave":
054e4681667c planemo upload lecorguille parents: diff changeset	35 ppm $methods.ppm
054e4681667c planemo upload lecorguille parents: diff changeset	36 peakwidth "c($methods.peakwidth)"
6 0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	37 #if $methods.options_c.option == "show":
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	38 mzdiff $methods.options_c.mzdiff
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	39 snthresh $methods.options_c.snthresh
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	40 integrate $methods.options_c.integrate
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	41 noise $methods.options_c.noise
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	42 prefilter "c($methods.options_c.prefilter)"
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	43 #end if
0 054e4681667c planemo upload lecorguille parents: diff changeset	44 #elif $methods.method == "matchedFilter":
054e4681667c planemo upload lecorguille parents: diff changeset	45 step $methods.step
054e4681667c planemo upload lecorguille parents: diff changeset	46 fwhm $methods.fwhm
054e4681667c planemo upload lecorguille parents: diff changeset	47 #if $methods.options_m.option == "show":
054e4681667c planemo upload lecorguille parents: diff changeset	48 ## sigma "$methods.options_m.sigma"
054e4681667c planemo upload lecorguille parents: diff changeset	49 max $methods.options_m.max
054e4681667c planemo upload lecorguille parents: diff changeset	50 snthresh $methods.options_m.snthresh
054e4681667c planemo upload lecorguille parents: diff changeset	51 steps $methods.options_m.steps
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	52 mzdiff $methods.options_m.mzdiff
0 054e4681667c planemo upload lecorguille parents: diff changeset	53 #end if
054e4681667c planemo upload lecorguille parents: diff changeset	54 #elif $methods.method == "MSW":
054e4681667c planemo upload lecorguille parents: diff changeset	55 snthr $methods.snthr
054e4681667c planemo upload lecorguille parents: diff changeset	56 nearbyPeak $methods.nearbyPeak
054e4681667c planemo upload lecorguille parents: diff changeset	57 winSize.noise $methods.winSize_noise
054e4681667c planemo upload lecorguille parents: diff changeset	58 amp.Th $methods.amp_Th
054e4681667c planemo upload lecorguille parents: diff changeset	59 scales "c($methods.scales)"
054e4681667c planemo upload lecorguille parents: diff changeset	60 SNR.method "$methods.SNR_method"
054e4681667c planemo upload lecorguille parents: diff changeset	61 #end if
6 0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	62 @COMMAND_LOG_EXIT@
5 588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	63 ]]></command>
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	64
0 054e4681667c planemo upload lecorguille parents: diff changeset	65 <inputs>
054e4681667c planemo upload lecorguille parents: diff changeset	66
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	67 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
0 054e4681667c planemo upload lecorguille parents: diff changeset	68
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	69 <conditional name="options_scanrange">
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	70 <param name="option" type="select" label="Scan range option " >
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	71 <option value="show">show</option>
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	72 <option value="hide" selected="true">hide</option>
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	73 </param>
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	74 <when value="show">
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	75 <param name="scanrange" type="text" value="" label="scanrange" help="scan range to process, for example (16,365)" >
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	76 <validator type="empty_field"/>
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	77 </param>
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	78 </when>
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	79 <when value="hide">
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	80 </when>
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	81 </conditional>
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	82
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	83
0 054e4681667c planemo upload lecorguille parents: diff changeset	84 <!--
054e4681667c planemo upload lecorguille parents: diff changeset	85 <param name="profmethod" type="select" label="Method to use for profile generation (profmethod)" >
054e4681667c planemo upload lecorguille parents: diff changeset	86 <option value="bin" selected="true">bin</option>
054e4681667c planemo upload lecorguille parents: diff changeset	87 <option value="binlin">binlin</option>
054e4681667c planemo upload lecorguille parents: diff changeset	88 <option value="binlinbase">binlinbase</option>
054e4681667c planemo upload lecorguille parents: diff changeset	89 <option value="intlin">intlin</option>
054e4681667c planemo upload lecorguille parents: diff changeset	90 </param>
054e4681667c planemo upload lecorguille parents: diff changeset	91 -->
054e4681667c planemo upload lecorguille parents: diff changeset	92 <conditional name="methods">
054e4681667c planemo upload lecorguille parents: diff changeset	93 <param name="method" type="select" label="Extraction method for peaks detection" help="[method] See the help section below">
054e4681667c planemo upload lecorguille parents: diff changeset	94 <option value="centWave" >centWave</option>
054e4681667c planemo upload lecorguille parents: diff changeset	95 <option value="matchedFilter" selected="true">matchedFilter</option>
054e4681667c planemo upload lecorguille parents: diff changeset	96 <option value="MSW">MSW</option>
054e4681667c planemo upload lecorguille parents: diff changeset	97 </param>
054e4681667c planemo upload lecorguille parents: diff changeset	98
054e4681667c planemo upload lecorguille parents: diff changeset	99 <!-- centWave Filter options -->
054e4681667c planemo upload lecorguille parents: diff changeset	100 <when value="centWave">
054e4681667c planemo upload lecorguille parents: diff changeset	101 <param name="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" />
054e4681667c planemo upload lecorguille parents: diff changeset	102 <param name="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="[peakwidth]" />
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	103
0 054e4681667c planemo upload lecorguille parents: diff changeset	104 <conditional name="options_c">
054e4681667c planemo upload lecorguille parents: diff changeset	105 <param name="option" type="select" label="Advanced options" >
054e4681667c planemo upload lecorguille parents: diff changeset	106 <option value="show">show</option>
054e4681667c planemo upload lecorguille parents: diff changeset	107 <option value="hide" selected="true">hide</option>
054e4681667c planemo upload lecorguille parents: diff changeset	108 </param>
054e4681667c planemo upload lecorguille parents: diff changeset	109 <when value="show">
054e4681667c planemo upload lecorguille parents: diff changeset	110 <param name="snthresh" type="integer" value="10" label="Signal/Noise threshold" help="[snthresh] Signal to noise ratio cutoff" />
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	111 <param name="mzdiff" type="float" value="-0.001" label="Minimum difference in m/z for peaks with overlapping retention times" help="[mzdiff] Can be negative to allow overlap" />
0 054e4681667c planemo upload lecorguille parents: diff changeset	112 <param name="integrate" type="select" label="peak limits method" help="[integrate]" >
054e4681667c planemo upload lecorguille parents: diff changeset	113 <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option>
054e4681667c planemo upload lecorguille parents: diff changeset	114 <option value="2">peak limits based on real data (more sensitive to noise)</option>
054e4681667c planemo upload lecorguille parents: diff changeset	115 </param>
054e4681667c planemo upload lecorguille parents: diff changeset	116 <param name="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="[prefilter] Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/>
054e4681667c planemo upload lecorguille parents: diff changeset	117 <param name="noise" type="integer" value="0" label="Noise filter" help="[noise] optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity smaller than ‘noise’ are omitted from ROI detection"/>
054e4681667c planemo upload lecorguille parents: diff changeset	118 </when>
5 588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	119 <when value="hide">
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	120 </when>
0 054e4681667c planemo upload lecorguille parents: diff changeset	121 </conditional>
054e4681667c planemo upload lecorguille parents: diff changeset	122 </when>
054e4681667c planemo upload lecorguille parents: diff changeset	123
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	124 <!-- matched Filter options -->
0 054e4681667c planemo upload lecorguille parents: diff changeset	125 <when value="matchedFilter">
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	126 <param name="step" type="float" value="0.1" label="Step size to use for profile generation" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" />
0 054e4681667c planemo upload lecorguille parents: diff changeset	127 <param name="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="[fwhm] Only used to calculate the actual sigma" />
054e4681667c planemo upload lecorguille parents: diff changeset	128 <conditional name="options_m">
054e4681667c planemo upload lecorguille parents: diff changeset	129 <param name="option" type="select" label="Advanced options" >
054e4681667c planemo upload lecorguille parents: diff changeset	130 <option value="show">show</option>
054e4681667c planemo upload lecorguille parents: diff changeset	131 <option value="hide" selected="true">hide</option>
054e4681667c planemo upload lecorguille parents: diff changeset	132 </param>
054e4681667c planemo upload lecorguille parents: diff changeset	133 <when value="show">
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	134 <!--<param name="sigma" type="float" value="12.739935451" label="Standard deviation (width) of matched filtration model peak" help="[sigma] By default: fwhm/2.3548" />-->
0 054e4681667c planemo upload lecorguille parents: diff changeset	135 <param name="max" type="integer" value="5" label="Maximum number of peaks per extracted ion chromatogram" help="[max]" />
054e4681667c planemo upload lecorguille parents: diff changeset	136 <param name="snthresh" type="integer" value="10" label="Signal to noise ratio cutoff" help="[snthresh]" />
054e4681667c planemo upload lecorguille parents: diff changeset	137 <param name="steps" type="integer" value="2" label="Number of steps to merge prior to filtration" help="[steps] The peak identification algorithm combines a given number of EIBPCs prior to filtration and peak detection, as defined by the steps argument" />
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	138 <param name="mzdiff" type="float" value="0.6" label="Minimum difference in m/z for peaks with overlapping Retention Times" help="[mzdiff] By default: 0.8-step*steps " />
0 054e4681667c planemo upload lecorguille parents: diff changeset	139 </when>
5 588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	140 <when value="hide">
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	141 </when>
0 054e4681667c planemo upload lecorguille parents: diff changeset	142 </conditional>
054e4681667c planemo upload lecorguille parents: diff changeset	143 </when>
054e4681667c planemo upload lecorguille parents: diff changeset	144
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	145 <!-- MSW Filter options -->
0 054e4681667c planemo upload lecorguille parents: diff changeset	146 <when value="MSW">
054e4681667c planemo upload lecorguille parents: diff changeset	147 <param name="nearbyPeak" type="select" label="Determine whether to include the nearby small peaks of major peaks" help="[nearbyPeak]" >
054e4681667c planemo upload lecorguille parents: diff changeset	148 <option value="TRUE">TRUE</option>
054e4681667c planemo upload lecorguille parents: diff changeset	149 <option value="FALSE">FALSE</option>
054e4681667c planemo upload lecorguille parents: diff changeset	150 </param>
054e4681667c planemo upload lecorguille parents: diff changeset	151 <param name="winSize_noise" type="integer" value="500" label="The local window size to estimate the noise level" help="[winSize.noise]" />
054e4681667c planemo upload lecorguille parents: diff changeset	152 <param name="snthr" type="integer" value="3" label="SNR (Signal to Noise Ratio) threshold" help="[snthr]" />
054e4681667c planemo upload lecorguille parents: diff changeset	153 <param name="amp_Th" type="float" value="0.002" label="Minimum required relative amplitude of the peak" help="[amp.Th] Ratio to the maximum of CWT coefficients" />
054e4681667c planemo upload lecorguille parents: diff changeset	154 <param name="scales" type="text" value="seq(1,22,3)" label="Scales for the Continuous Wavelet Transform (CWT)" help="[scales] Scales are linked to the width of the peaks that are to be detected. Tape as indicaded seq('n,n,n') or c(n,n) : seq(from, to, by steps), c - linear vector " />
054e4681667c planemo upload lecorguille parents: diff changeset	155 <param name="SNR_method" type="text" value="data.mean" label="SNR (Signal to Noise Ratio) method" help="[SNR.method] Method to estimate noise level. Currently, only 95 percentage quantile is supported." />
054e4681667c planemo upload lecorguille parents: diff changeset	156 </when>
054e4681667c planemo upload lecorguille parents: diff changeset	157 </conditional>
054e4681667c planemo upload lecorguille parents: diff changeset	158 </inputs>
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	159
0 054e4681667c planemo upload lecorguille parents: diff changeset	160 <outputs>
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	161 <data name="xsetRData" format="rdata.xcms.raw" label="${input.name.rsplit('.',1)[0]}.xset.RData" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	162 <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv">
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	163 <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	164 </data>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	165 <data name="ticsRawPdf" format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.pdf" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	166 <data name="bpcsRawPdf" format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.pdf" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	167 <data name="log" format="txt" label="${input.name.rsplit('.',1)[0]}.xset.log.txt" />
0 054e4681667c planemo upload lecorguille parents: diff changeset	168 </outputs>
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	169
0 054e4681667c planemo upload lecorguille parents: diff changeset	170 <tests>
7 451ff602a957 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	171 <!--<test>
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	172 <param name="input" value="sacuri_dir_root.zip" ftype="zip" />
6 0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	173 <param name="methods\|method" value="matchedFilter" />
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	174 <param name="methods\|step" value="0.01" />
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	175 <param name="methods\|fwhm" value="4" />
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	176 <param name="methods\|options_m\|option" value="show" />
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	177 <param name="methods\|options_m\|max" value="50" />
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	178 <param name="methods\|options_m\|snthresh" value="1" />
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	179 <param name="methods\|options_m\|steps" value="2" />
5 588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	180 <output name="log">
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	181 <assert_contents>
6 0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	182 <has_text text="object with 4 samples" />
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	183 <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	184 <has_text text="Mass range: 50.0021-999.9863 m/z" />
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	185 <has_text text="Peaks: 59359 (about 14840 per sample)" />
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	186 <has_text text="Peak Groups: 0" />
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	187 <has_text text="Sample classes: bio, blank" />
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	188 </assert_contents>
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	189 </output>
7 451ff602a957 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	190 </test>
6 0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	191 <test>
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	192 <param name="input" value="sacuri_current_root.zip" ftype="zip" />
6 0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	193 <param name="methods\|method" value="centWave" />
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	194 <param name="methods\|ppm" value="25" />
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	195 <param name="methods\|peakwidth" value="20,50" />
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	196 <output name="log">
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	197 <assert_contents>
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	198 <has_text text="object with 4 samples" />
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	199 <has_text text="Time range: 3.5-1139.2 seconds (0.1-19 minutes)" />
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	200 <has_text text="Mass range: 57.9756-593.4086 m/z" />
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	201 <has_text text="Peaks: 1535 (about 384 per sample)" />
5 588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	202 <has_text text="Peak Groups: 0" />
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	203 <has_text text="Sample classes: bio, blank" />
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	204 </assert_contents>
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	205 </output>
7 451ff602a957 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	206 </test>-->
451ff602a957 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	207 <test>
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	208 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
7 451ff602a957 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	209 <param name="methods\|method" value="centWave" />
451ff602a957 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	210 <param name="methods\|ppm" value="25" />
451ff602a957 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	211 <param name="methods\|peakwidth" value="20,50" />
451ff602a957 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	212 <output name="log">
451ff602a957 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	213 <assert_contents>
451ff602a957 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	214 <has_text text="object with 4 samples" />
451ff602a957 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	215 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
451ff602a957 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	216 <has_text text="Mass range: 200.1-600 m/z" />
451ff602a957 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	217 <has_text text="Peaks: 9251 (about 2313 per sample)" />
451ff602a957 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	218 <has_text text="Peak Groups: 0" />
451ff602a957 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	219 <has_text text="Sample classes: KO, WT" />
451ff602a957 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	220 </assert_contents>
451ff602a957 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	221 </output>
0 054e4681667c planemo upload lecorguille parents: diff changeset	222 </test>
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	223 <!-- Passed but disable to save time for Travis" -->
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	224 <!--<test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	225 <param name="input" value="ko15.CDF" ftype="netcdf" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	226 <param name="methods\|method" value="centWave" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	227 <param name="methods\|ppm" value="25" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	228 <param name="methods\|peakwidth" value="20,50" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	229 <output name="log">
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	230 <assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	231 <has_text text="object with 1 samples" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	232 <has_text text="Time range: 2506.1-4471.7 seconds (41.8-74.5 minutes)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	233 <has_text text="Mass range: 200.2-600 m/z" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	234 <has_text text="Peaks: 2262 (about 2262 per sample)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	235 <has_text text="Peak Groups: 0" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	236 <has_text text="Sample classes: ." />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	237 </assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	238 </output>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	239 </test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	240 <test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	241 <param name="input" value="ko16.CDF" ftype="netcdf" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	242 <param name="methods\|method" value="centWave" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	243 <param name="methods\|ppm" value="25" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	244 <param name="methods\|peakwidth" value="20,50" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	245 <output name="log">
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	246 <assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	247 <has_text text="object with 1 samples" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	248 <has_text text="Time range: 2521.7-4477.9 seconds (42-74.6 minutes)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	249 <has_text text="Mass range: 200.1-600 m/z" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	250 <has_text text="Peaks: 2408 (about 2408 per sample)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	251 <has_text text="Peak Groups: 0" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	252 <has_text text="Sample classes: ." />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	253 </assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	254 </output>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	255 </test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	256 <test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	257 <param name="input" value="wt15.CDF" ftype="netcdf" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	258 <param name="methods\|method" value="centWave" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	259 <param name="methods\|ppm" value="25" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	260 <param name="methods\|peakwidth" value="20,50" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	261 <output name="log">
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	262 <assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	263 <has_text text="object with 1 samples" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	264 <has_text text="Time range: 2517-4473.2 seconds (42-74.6 minutes)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	265 <has_text text="Mass range: 200.2-599.8 m/z" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	266 <has_text text="Peaks: 2278 (about 2278 per sample)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	267 <has_text text="Peak Groups: 0" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	268 <has_text text="Sample classes: ." />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	269 </assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	270 </output>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	271 </test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	272 <test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	273 <param name="inputs\|input" value="single_file" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	274 <param name="inputs\|single_file" value="wt16.CDF" ftype="netcdf" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	275 <param name="methods\|method" value="centWave" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	276 <param name="methods\|ppm" value="25" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	277 <param name="methods\|peakwidth" value="20,50" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	278 <output name="log">
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	279 <assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	280 <has_text text="object with 1 samples" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	281 <has_text text="Time range: 2521.7-4468.5 seconds (42-74.5 minutes)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	282 <has_text text="Mass range: 200.3-600 m/z" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	283 <has_text text="Peaks: 2303 (about 2303 per sample)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	284 <has_text text="Peak Groups: 0" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	285 <has_text text="Sample classes: ." />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	286 </assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	287 </output>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	288 </test>-->
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	289 <test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	290 <param name="input" value="HU_neg_017.mzXML" ftype="mzxml" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	291 <param name="methods\|method" value="centWave" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	292 <param name="methods\|ppm" value="25" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	293 <param name="methods\|peakwidth" value="20,50" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	294 <output name="log">
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	295 <assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	296 <has_text text="object with 1 samples" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	297 <has_text text="Time range: 3.5-1139.1 seconds (0.1-19 minutes)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	298 <has_text text="Mass range: 57.9756-556.8128 m/z" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	299 <has_text text="Peaks: 380 (about 380 per sample)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	300 <has_text text="Peak Groups: 0" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	301 <has_text text="Sample classes: ." />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	302 </assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	303 </output>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	304 </test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	305 <test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	306 <param name="input" value="MM14.mzML" ftype="mzxml" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	307 <param name="methods\|method" value="centWave" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	308 <param name="methods\|ppm" value="56" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	309 <param name="methods\|peakwidth" value="5.275,13.5" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	310 <output name="log">
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	311 <assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	312 <has_text text="object with 1 samples" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	313 <has_text text="Time range: 271-307.3 seconds (4.5-5.1 minutes)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	314 <has_text text="Mass range: 117.0357-936.7059 m/z" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	315 <has_text text="Peaks: 222 (about 222 per sample)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	316 <has_text text="Peak Groups: 0" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	317 <has_text text="Sample classes: ." />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	318 </assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	319 </output>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	320 </test>
0 054e4681667c planemo upload lecorguille parents: diff changeset	321 </tests>
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	322
5 588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	323 <help><![CDATA[
0 054e4681667c planemo upload lecorguille parents: diff changeset	324
6 0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	325 @HELP_AUTHORS@
0 054e4681667c planemo upload lecorguille parents: diff changeset	326
054e4681667c planemo upload lecorguille parents: diff changeset	327 ============
054e4681667c planemo upload lecorguille parents: diff changeset	328 Xcms.xcmsSet
054e4681667c planemo upload lecorguille parents: diff changeset	329 ============
054e4681667c planemo upload lecorguille parents: diff changeset	330
054e4681667c planemo upload lecorguille parents: diff changeset	331 -----------
054e4681667c planemo upload lecorguille parents: diff changeset	332 Description
054e4681667c planemo upload lecorguille parents: diff changeset	333 -----------
054e4681667c planemo upload lecorguille parents: diff changeset	334
054e4681667c planemo upload lecorguille parents: diff changeset	335 This tool is used for preprocessing analyte data from multiple LC/MS files (formats NetCDF, mzXML and mzData). It extracts ion from each sample independently and using a statistic model, peaks are filtered and integrated.
054e4681667c planemo upload lecorguille parents: diff changeset	336 You can read a tutorial on how to perform xcms preprocessing which is available here_.
054e4681667c planemo upload lecorguille parents: diff changeset	337
054e4681667c planemo upload lecorguille parents: diff changeset	338 .. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf
054e4681667c planemo upload lecorguille parents: diff changeset	339
054e4681667c planemo upload lecorguille parents: diff changeset	340
054e4681667c planemo upload lecorguille parents: diff changeset	341 -----------------
054e4681667c planemo upload lecorguille parents: diff changeset	342 Workflow position
054e4681667c planemo upload lecorguille parents: diff changeset	343 -----------------
054e4681667c planemo upload lecorguille parents: diff changeset	344
054e4681667c planemo upload lecorguille parents: diff changeset	345 Upstream tools
054e4681667c planemo upload lecorguille parents: diff changeset	346
054e4681667c planemo upload lecorguille parents: diff changeset	347 ========================= ================= ======= =========
054e4681667c planemo upload lecorguille parents: diff changeset	348 Name output file format parameter
054e4681667c planemo upload lecorguille parents: diff changeset	349 ========================= ================= ======= =========
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	350 NA NA zip NA
0 054e4681667c planemo upload lecorguille parents: diff changeset	351 ========================= ================= ======= =========
054e4681667c planemo upload lecorguille parents: diff changeset	352
054e4681667c planemo upload lecorguille parents: diff changeset	353
054e4681667c planemo upload lecorguille parents: diff changeset	354 Downstream tools
054e4681667c planemo upload lecorguille parents: diff changeset	355
054e4681667c planemo upload lecorguille parents: diff changeset	356 +---------------------------+--------------------+-----------------+
054e4681667c planemo upload lecorguille parents: diff changeset	357 \| Name \| Output file \| Format \|
054e4681667c planemo upload lecorguille parents: diff changeset	358 +===========================+====================+=================+
054e4681667c planemo upload lecorguille parents: diff changeset	359 \|xcms.group \| xset.RData \| rdata.xcms.raw \|
054e4681667c planemo upload lecorguille parents: diff changeset	360 +---------------------------+--------------------+-----------------+
054e4681667c planemo upload lecorguille parents: diff changeset	361 \|PCA ellipsoid by factors \| sampleMetadata.tsv \| Tabular \|
054e4681667c planemo upload lecorguille parents: diff changeset	362 +---------------------------+--------------------+-----------------+
054e4681667c planemo upload lecorguille parents: diff changeset	363 \|Anova \| sampleMetadata.tsv \| Tabular \|
054e4681667c planemo upload lecorguille parents: diff changeset	364 +---------------------------+--------------------+-----------------+
054e4681667c planemo upload lecorguille parents: diff changeset	365
054e4681667c planemo upload lecorguille parents: diff changeset	366
054e4681667c planemo upload lecorguille parents: diff changeset	367 Example of a metabolomic workflow
054e4681667c planemo upload lecorguille parents: diff changeset	368
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	369 .. image:: xcms_xcmsset_workflow.png
0 054e4681667c planemo upload lecorguille parents: diff changeset	370
054e4681667c planemo upload lecorguille parents: diff changeset	371
054e4681667c planemo upload lecorguille parents: diff changeset	372 ------
054e4681667c planemo upload lecorguille parents: diff changeset	373
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	374 .. class:: infomark
0 054e4681667c planemo upload lecorguille parents: diff changeset	375
054e4681667c planemo upload lecorguille parents: diff changeset	376 The output file is an xset.RData file. You can continue your analysis using it in xcms.group tool.
054e4681667c planemo upload lecorguille parents: diff changeset	377
054e4681667c planemo upload lecorguille parents: diff changeset	378 ---------------------------------------------------
054e4681667c planemo upload lecorguille parents: diff changeset	379
054e4681667c planemo upload lecorguille parents: diff changeset	380
054e4681667c planemo upload lecorguille parents: diff changeset	381
054e4681667c planemo upload lecorguille parents: diff changeset	382 -----------
054e4681667c planemo upload lecorguille parents: diff changeset	383 Input files
054e4681667c planemo upload lecorguille parents: diff changeset	384 -----------
054e4681667c planemo upload lecorguille parents: diff changeset	385
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	386 +---------------------------+----------------------------------+
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	387 \| Parameter : num + label \| Format \|
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	388 +===========================+==================================+
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	389 \| OR : Zip file \| zip \|
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	390 +---------------------------+----------------------------------+
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	391 \| OR : Single file \| mzXML, mzML, mzData, netCDF \|
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	392 +---------------------------+----------------------------------+
0 054e4681667c planemo upload lecorguille parents: diff changeset	393
054e4681667c planemo upload lecorguille parents: diff changeset	394 Choose your inputs
054e4681667c planemo upload lecorguille parents: diff changeset	395
054e4681667c planemo upload lecorguille parents: diff changeset	396 You have two methods for your inputs:
054e4681667c planemo upload lecorguille parents: diff changeset	397
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	398 \| Single file (recommended): You can put a single file as input. That way, you will be able to launch several xcmsSet in parallel and use "xcms.xcmsSet Merger" before "xcms.group"
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	399 \| Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
0 054e4681667c planemo upload lecorguille parents: diff changeset	400
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	401 Zip file: Steps for creating the zip file
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	402 -----------------------------------------
5 588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	403
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	404 Step1: Creating your directory and hierarchize the subdirectories
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	405
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	406
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	407 VERY IMPORTANT: If you zip your files under Windows, you must use the 7Zip software (http://www.7-zip.org/), otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug).
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	408
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	409 Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	410 arabidopsis/wild/01.raw
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	411 arabidopsis/mutant/01.raw
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	412
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	413 Step2: Creating a zip file
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	414
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	415 Create your zip file (e.g.: arabidopsis.zip).
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	416
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	417 Step 3 : Uploading it to our Galaxy server
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	418
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	419 If your zip file is less than 2Gb, you get use the Get Data tool to upload it.
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	420
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	421 Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO on workflow4metabolomics.org (http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf).
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	422
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	423 For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	424
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	425 Advices for converting your files for the XCMS input
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	426 ----------------------------------------------------
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	427
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	428 We recommend you to convert your raw files to mzXML in centroid mode (smaller files) and the files will be compatible with the xmcs centWave method.
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	429
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	430 We recommend you the following parameters:
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	431
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	432 Use Filtering: True
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	433
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	434 Use Peak Picking: True
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	435
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	436 Peak Peaking -Apply to MS Levels: All Levels (1-) : Centroid Mode
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	437
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	438 Use zlib: 64
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	439
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	440 Binary Encoding: 64
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	441
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	442 m/z Encoding: 64
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	443
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	444 Intensity Encoding: 64
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	445
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	446
0 054e4681667c planemo upload lecorguille parents: diff changeset	447 ----------
054e4681667c planemo upload lecorguille parents: diff changeset	448 Parameters
054e4681667c planemo upload lecorguille parents: diff changeset	449 ----------
054e4681667c planemo upload lecorguille parents: diff changeset	450
054e4681667c planemo upload lecorguille parents: diff changeset	451 Extraction method for peaks detection
054e4681667c planemo upload lecorguille parents: diff changeset	452 -------------------------------------
054e4681667c planemo upload lecorguille parents: diff changeset	453
054e4681667c planemo upload lecorguille parents: diff changeset	454 Matched Filter
054e4681667c planemo upload lecorguille parents: diff changeset	455
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	456 \| One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm.
0 054e4681667c planemo upload lecorguille parents: diff changeset	457 \| For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002).
054e4681667c planemo upload lecorguille parents: diff changeset	458
054e4681667c planemo upload lecorguille parents: diff changeset	459
054e4681667c planemo upload lecorguille parents: diff changeset	460 cent Wave
054e4681667c planemo upload lecorguille parents: diff changeset	461
054e4681667c planemo upload lecorguille parents: diff changeset	462 \| This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode.
054e4681667c planemo upload lecorguille parents: diff changeset	463 \| Due to the fact that peak centroids are used, a binning step is not necessary.
054e4681667c planemo upload lecorguille parents: diff changeset	464 \| The method is capable of detecting close-by-peaks and also overlapping peaks. Some efforts are made to detect the exact peak boundaries to get precise peak integrals.
054e4681667c planemo upload lecorguille parents: diff changeset	465
054e4681667c planemo upload lecorguille parents: diff changeset	466 MSW
054e4681667c planemo upload lecorguille parents: diff changeset	467
054e4681667c planemo upload lecorguille parents: diff changeset	468 \| Wavelet based, used for direct infusion data. Continuous wavelet transform (CWT) can be used to locate chromatographic peaks on different scales.
054e4681667c planemo upload lecorguille parents: diff changeset	469 \| If you wish to have more details about the other parameters, you can read the following documents:
054e4681667c planemo upload lecorguille parents: diff changeset	470 \| -Example of preprocessing data with XCMS : http://www.bioconductor.org/packages/2.12/bioc/vignettes/xcms/inst/doc/xcmsPreprocess.pdf
054e4681667c planemo upload lecorguille parents: diff changeset	471 \| -Details and explanations for all the parameters of XCMS package: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf
054e4681667c planemo upload lecorguille parents: diff changeset	472
054e4681667c planemo upload lecorguille parents: diff changeset	473
054e4681667c planemo upload lecorguille parents: diff changeset	474 ------------
054e4681667c planemo upload lecorguille parents: diff changeset	475 Output files
054e4681667c planemo upload lecorguille parents: diff changeset	476 ------------
054e4681667c planemo upload lecorguille parents: diff changeset	477
054e4681667c planemo upload lecorguille parents: diff changeset	478 xset.TICs_raw.pdf
054e4681667c planemo upload lecorguille parents: diff changeset	479
054e4681667c planemo upload lecorguille parents: diff changeset	480 \| "Total Ion Chromatograms" graph in pdf format.
054e4681667c planemo upload lecorguille parents: diff changeset	481
054e4681667c planemo upload lecorguille parents: diff changeset	482 xset.BPCs_raw.pdf
054e4681667c planemo upload lecorguille parents: diff changeset	483
054e4681667c planemo upload lecorguille parents: diff changeset	484 \| "Base Peak Chromatograms" graph in pdf format with each class samples opposed.
054e4681667c planemo upload lecorguille parents: diff changeset	485
054e4681667c planemo upload lecorguille parents: diff changeset	486 sampleMetadata.tsv
054e4681667c planemo upload lecorguille parents: diff changeset	487
054e4681667c planemo upload lecorguille parents: diff changeset	488 \| Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed).
054e4681667c planemo upload lecorguille parents: diff changeset	489 \| This file is necessary in the Anova and PCA step of the workflow.
054e4681667c planemo upload lecorguille parents: diff changeset	490
054e4681667c planemo upload lecorguille parents: diff changeset	491 xset.RData: rdata.xcms.raw format
054e4681667c planemo upload lecorguille parents: diff changeset	492
054e4681667c planemo upload lecorguille parents: diff changeset	493 \| Rdata file that is necessary in the second step of the workflow "xcms.group".
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	494
0 054e4681667c planemo upload lecorguille parents: diff changeset	495 ------
054e4681667c planemo upload lecorguille parents: diff changeset	496
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	497 .. class:: infomark
0 054e4681667c planemo upload lecorguille parents: diff changeset	498
054e4681667c planemo upload lecorguille parents: diff changeset	499 The output file is an xset.RData file. You can continue your analysis using it in xcms.group tool.
054e4681667c planemo upload lecorguille parents: diff changeset	500
054e4681667c planemo upload lecorguille parents: diff changeset	501 ---------------------------------------------------
054e4681667c planemo upload lecorguille parents: diff changeset	502
054e4681667c planemo upload lecorguille parents: diff changeset	503 ---------------
054e4681667c planemo upload lecorguille parents: diff changeset	504 Working example
054e4681667c planemo upload lecorguille parents: diff changeset	505 ---------------
054e4681667c planemo upload lecorguille parents: diff changeset	506
054e4681667c planemo upload lecorguille parents: diff changeset	507 Input files
054e4681667c planemo upload lecorguille parents: diff changeset	508 -----------
054e4681667c planemo upload lecorguille parents: diff changeset	509
054e4681667c planemo upload lecorguille parents: diff changeset	510 \| zip_file -> sacuri.zip
054e4681667c planemo upload lecorguille parents: diff changeset	511
054e4681667c planemo upload lecorguille parents: diff changeset	512 Parameters
054e4681667c planemo upload lecorguille parents: diff changeset	513 ----------
054e4681667c planemo upload lecorguille parents: diff changeset	514
054e4681667c planemo upload lecorguille parents: diff changeset	515 \| Method -> matchedFilter
054e4681667c planemo upload lecorguille parents: diff changeset	516 \| step -> 0.01
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	517 \| fwhm -> 4
0 054e4681667c planemo upload lecorguille parents: diff changeset	518 \| Advanced option -> show
054e4681667c planemo upload lecorguille parents: diff changeset	519 \| max: -> 50
054e4681667c planemo upload lecorguille parents: diff changeset	520 \| snthresh -> 1
054e4681667c planemo upload lecorguille parents: diff changeset	521 \| steps -> 2
054e4681667c planemo upload lecorguille parents: diff changeset	522
054e4681667c planemo upload lecorguille parents: diff changeset	523
054e4681667c planemo upload lecorguille parents: diff changeset	524 Output files
054e4681667c planemo upload lecorguille parents: diff changeset	525 ------------
054e4681667c planemo upload lecorguille parents: diff changeset	526
054e4681667c planemo upload lecorguille parents: diff changeset	527 \| 1) xset.RData: RData file
054e4681667c planemo upload lecorguille parents: diff changeset	528
054e4681667c planemo upload lecorguille parents: diff changeset	529 \| 2) Example of a sampleMetadata.tsv :
054e4681667c planemo upload lecorguille parents: diff changeset	530
054e4681667c planemo upload lecorguille parents: diff changeset	531
054e4681667c planemo upload lecorguille parents: diff changeset	532 +---------------------------+------------+---------+
054e4681667c planemo upload lecorguille parents: diff changeset	533 \| sampleMetadata \| class \| polarity\|
054e4681667c planemo upload lecorguille parents: diff changeset	534 +===========================+============+=========+
054e4681667c planemo upload lecorguille parents: diff changeset	535 \|HU_neg_017 \| bio \|negative \|
054e4681667c planemo upload lecorguille parents: diff changeset	536 +---------------------------+------------+---------+
054e4681667c planemo upload lecorguille parents: diff changeset	537 \|HU_neg_028 \| bio \|negative \|
054e4681667c planemo upload lecorguille parents: diff changeset	538 +---------------------------+------------+---------+
054e4681667c planemo upload lecorguille parents: diff changeset	539 \|HU_neg_034 \| bio \|negative \|
054e4681667c planemo upload lecorguille parents: diff changeset	540 +---------------------------+------------+---------+
054e4681667c planemo upload lecorguille parents: diff changeset	541 \|Blanc04 \| blank \|negative \|
054e4681667c planemo upload lecorguille parents: diff changeset	542 +---------------------------+------------+---------+
054e4681667c planemo upload lecorguille parents: diff changeset	543 \|Blanc06 \| blank \|negative \|
054e4681667c planemo upload lecorguille parents: diff changeset	544 +---------------------------+------------+---------+
054e4681667c planemo upload lecorguille parents: diff changeset	545 \|Blanc09 \| blank \|negative \|
054e4681667c planemo upload lecorguille parents: diff changeset	546 +---------------------------+------------+---------+
054e4681667c planemo upload lecorguille parents: diff changeset	547
054e4681667c planemo upload lecorguille parents: diff changeset	548
054e4681667c planemo upload lecorguille parents: diff changeset	549
054e4681667c planemo upload lecorguille parents: diff changeset	550 \| 3) Example of xset.TICs_raw.pdf (Total Ion Chromatograms) :
054e4681667c planemo upload lecorguille parents: diff changeset	551
054e4681667c planemo upload lecorguille parents: diff changeset	552 .. image:: xcms_tics.png
054e4681667c planemo upload lecorguille parents: diff changeset	553
054e4681667c planemo upload lecorguille parents: diff changeset	554
5 588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	555 ---------------------------------------------------
4 c5fa73f1703f Uploaded mmonsoor parents: 0 diff changeset	556
5 588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	557 Changelog/News
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	558 --------------
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	559
13 c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	560 Version 2.1.1 - 29/11/2017
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	561
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	562 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	563
12 15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	564 Version 2.1.0 - 22/02/2017
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	565
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	566 - NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group".
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	567
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	568 - BUGFIX: the default value of "matchedFilter" -> "Step size to use for profile generation" which was of 0.01 have been changed to fix with the XMCS default values to 0.1
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 lecorguille parents: 11 diff changeset	569
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	570 Version 2.0.11 - 22/12/2016
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	571
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	572 - BUGFIX: propose scanrange for all methods
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	573
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	574 Version 2.0.10 - 22/12/2016
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	575
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	576 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	577
10 69eb0fc05837 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 7 diff changeset	578 Version 2.0.9 - 06/07/2016
69eb0fc05837 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 7 diff changeset	579
11 91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 10 diff changeset	580 - UPGRADE: upgrade the xcms version from 1.44.0 to 1.46.0
10 69eb0fc05837 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 7 diff changeset	581
6 0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	582 Version 2.0.8 - 06/04/2016
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	583
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	584 - TEST: refactoring to pass planemo test using conda dependencies
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	585
5 588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	586
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	587 Version 2.0.7 - 10/02/2016
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	588
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	589 - BUGFIX: better management of errors. Datasets remained green although the process failed
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	590
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	591 - BUGFIX/IMPROVEMENT: New checking steps around the imported data in order to raise explicte error message before or after launch XCMS: checking of bad characters in the filenames, checking of the XML integrity and checking of duplicates which can appear in the sample names during the XCMS process because of bad characters
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	592
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	593 - BUGFIX/IMPROVEMENT: New step to check and delete bad characters in the XML: accented characters in the storage path of the mass spectrometer
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	594
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	595 - UPDATE: refactoring of internal management of inputs/outputs
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	596
6 0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	597 - TEST: refactoring to feed the new report tool
5 588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	598
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	599
13 c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1 lecorguille parents: 12 diff changeset	600 Version 2.0.2 - 18/01/2016
5 588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	601
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	602 - BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	603
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	604
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	605 Version 2.0.2 - 09/10/2015
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	606
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	607 - BUGFIX: Some users reported a bug in xcms.xcmsSet. The preprocessing stops itself and doesn't import the whole dataset contained in the zip file without warning. But meanwhile, please check your samplemetadata dataset and the number of rows.
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	608
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	609
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	610 Version 2.0.2 - 02/06/2015
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	611
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	612 - NEW: The W4M workflows will now take as input a zip file to ease the transfer and to improve dataset exchange between tools and users. (See How_to_upload). The previous "Library directory name" is still available but we invite user to switch on the new zip system as soon as possible.
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	613
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	614 - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	615
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	616 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	617
588b0a7ae4b0 planemo upload lecorguille parents: 4 diff changeset	618 ]]></help>
0 054e4681667c planemo upload lecorguille parents: diff changeset	619
6 0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6 lecorguille parents: 5 diff changeset	620 <expand macro="citation" />
0 054e4681667c planemo upload lecorguille parents: diff changeset	621 </tool>

Mercurial > repos > lecorguille > xcms_xcmsset

annotate abims_xcms_xcmsSet.xml @ 13:c934dd5c49a9 draft