xcms_xcmsset: abims_xcms_xcmsSet.xml annotate

annotate abims_xcms_xcmsSet.xml @ 17:602acc32b549 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907

author	lecorguille
date	Sun, 05 Feb 2017 08:55:49 -0500
parents	f28041d2180a
children	d7971ea3ad1d

rev	line source
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	1 <tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.1.0">
0 1bad16e5e4ae 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>
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	3
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	4 <macros>
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	5 <import>macros.xml</import>
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	6 </macros>
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	7
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	8 <expand macro="requirements"/>
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	9 <expand macro="stdio"/>
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	10
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	11 <command><![CDATA[
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	12 @COMMAND_XCMS_SCRIPT@
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	13
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	14 #if $inputs.input == "zip_file":
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	15 zipfile $inputs.zip_file
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	16 #elif $inputs.input == "single_file":
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	17 singlefile_galaxyPath $inputs.single_file singlefile_sampleName $inputs.single_file.name
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	18 #end if
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	19
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	20 xfunction xcmsSet
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	21
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	22 xsetRdataOutput $xsetRData
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	23 sampleMetadataOutput $sampleMetadata
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	24 ticspdf $ticsRawPdf
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	25 bicspdf $bpcsRawPdf
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	26
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	27
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	28 #if $options_scanrange.option == "show":
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	29 scanrange "c($options_scanrange.scanrange)"
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	30 #end if
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	31
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	32 ## profmethod $profmethod
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	33 nSlaves \${GALAXY_SLOTS:-1} method $methods.method
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	34 #if $methods.method == "centWave":
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	35 ppm $methods.ppm
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	36 peakwidth "c($methods.peakwidth)"
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	37 #if $methods.options_c.option == "show":
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	38 mzdiff $methods.options_c.mzdiff
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	39 snthresh $methods.options_c.snthresh
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	40 integrate $methods.options_c.integrate
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	41 noise $methods.options_c.noise
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	42 prefilter "c($methods.options_c.prefilter)"
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	43 #end if
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	44 #elif $methods.method == "matchedFilter":
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	45 step $methods.step
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	46 fwhm $methods.fwhm
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	47 #if $methods.options_m.option == "show":
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	48 ## sigma "$methods.options_m.sigma"
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	49 max $methods.options_m.max
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	50 snthresh $methods.options_m.snthresh
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	51 ## mzdiff $methods.options_m.mzdiff
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	52 steps $methods.options_m.steps
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	53 ## sleep $methods.options_m.sleep
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	54 #end if
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	55 #elif $methods.method == "MSW":
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	56 snthr $methods.snthr
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	57 nearbyPeak $methods.nearbyPeak
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	58 winSize.noise $methods.winSize_noise
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	59 amp.Th $methods.amp_Th
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	60 scales "c($methods.scales)"
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	61 SNR.method "$methods.SNR_method"
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	62 #end if
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	63 @COMMAND_LOG_EXIT@
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	64 ]]></command>
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	65
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	66 <inputs>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	67
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	68 <conditional name="inputs">
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	69 <param name="input" type="select" label="Choose your inputs method" >
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	70 <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	71 <option value="single_file">mzXML file from your history</option>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	72 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	73 <when value="zip_file">
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	74 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	75 </when>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	76 <when value="single_file">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	77 <param name="single_file" type="data" format="mzxml,netcdf" label="Single file" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	78 </when>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	79 </conditional>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	80
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	81 <conditional name="options_scanrange">
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	82 <param name="option" type="select" label="Scan range option " >
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	83 <option value="show">show</option>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	84 <option value="hide" selected="true">hide</option>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	85 </param>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	86 <when value="show">
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	87 <param name="scanrange" type="text" value="" label="scanrange" help="scan range to process, for example (16,365)" >
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	88 <validator type="empty_field"/>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	89 </param>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	90 </when>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	91 <when value="hide">
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	92 </when>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	93 </conditional>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	94
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	95
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	96 <!--
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	97 <param name="profmethod" type="select" label="Method to use for profile generation (profmethod)" >
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	98 <option value="bin" selected="true">bin</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	99 <option value="binlin">binlin</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	100 <option value="binlinbase">binlinbase</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	101 <option value="intlin">intlin</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	102 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	103 -->
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	104 <conditional name="methods">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	105 <param name="method" type="select" label="Extraction method for peaks detection" help="[method] See the help section below">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	106 <option value="centWave" >centWave</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	107 <option value="matchedFilter" selected="true">matchedFilter</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	108 <option value="MSW">MSW</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	109 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	110
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	111 <!-- centWave Filter options -->
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	112 <when value="centWave">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	113 <param name="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	114 <param name="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="[peakwidth]" />
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	115
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	116 <conditional name="options_c">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	117 <param name="option" type="select" label="Advanced options" >
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	118 <option value="show">show</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	119 <option value="hide" selected="true">hide</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	120 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	121 <when value="show">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	122 <param name="snthresh" type="integer" value="10" label="Signal/Noise threshold" help="[snthresh] Signal to noise ratio cutoff" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	123 <param name="mzdiff" type="float" value="-0.001" label="Min m/z difference" help="[mzdiff] Min m/z difference for peaks with overlapping RT " />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	124 <param name="integrate" type="select" label="peak limits method" help="[integrate]" >
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	125 <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	126 <option value="2">peak limits based on real data (more sensitive to noise)</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	127 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	128 <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’"/>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	129 <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"/>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	130 </when>
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	131 <when value="hide">
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	132 </when>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	133 </conditional>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	134 </when>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	135
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	136 <!-- matched Filter options -->
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	137 <when value="matchedFilter">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	138 <param name="step" type="float" value="0.01" 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" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	139 <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" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	140 <conditional name="options_m">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	141 <param name="option" type="select" label="Advanced options" >
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	142 <option value="show">show</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	143 <option value="hide" selected="true">hide</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	144 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	145 <when value="show">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	146 <!--
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	147 <param name="sigma" type="hidden" value="fwhm/2.3548" label="sigma" help="standard deviation (fwhm/2.3548)" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	148 -->
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	149 <param name="max" type="integer" value="5" label="Maximum number of peaks per extracted ion chromatogram" help="[max]" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	150 <param name="snthresh" type="integer" value="10" label="Signal to noise ratio cutoff" help="[snthresh]" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	151 <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" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	152 <!--
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	153 <param name="mzdiff" type="text" size="20" value="0.8-step*steps" label="m/z difference" help="min m/z difference for peaks with overlapping RT " />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	154 -->
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	155 </when>
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	156 <when value="hide">
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	157 </when>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	158 </conditional>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	159 </when>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	160
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	161 <!-- MSW Filter options -->
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	162 <when value="MSW">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	163 <param name="nearbyPeak" type="select" label="Determine whether to include the nearby small peaks of major peaks" help="[nearbyPeak]" >
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	164 <option value="TRUE">TRUE</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	165 <option value="FALSE">FALSE</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	166 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	167 <param name="winSize_noise" type="integer" value="500" label="The local window size to estimate the noise level" help="[winSize.noise]" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	168 <param name="snthr" type="integer" value="3" label="SNR (Signal to Noise Ratio) threshold" help="[snthr]" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	169 <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" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	170 <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 " />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	171 <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." />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	172 </when>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	173 </conditional>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	174 </inputs>
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	175
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	176 <outputs>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	177 <data name="xsetRData" format="rdata.xcms.raw" label="xset.RData" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	178 <data name="sampleMetadata" format="tabular" label="sampleMetadata.tsv" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	179 <data name="ticsRawPdf" format="pdf" label="xset.TICs_raw.pdf" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	180 <data name="bpcsRawPdf" format="pdf" label="xset.BPCs_raw.pdf" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	181 <data name="log" format="txt" label="xset.log.txt" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	182 </outputs>
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	183
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	184 <tests>
10 00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	185 <!--<test>
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	186 <param name="inputs\|input" value="zip_file" />
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	187 <param name="inputs\|zip_file" value="sacuri_dir_root.zip" ftype="zip" />
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	188 <param name="methods\|method" value="matchedFilter" />
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	189 <param name="methods\|step" value="0.01" />
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	190 <param name="methods\|fwhm" value="4" />
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	191 <param name="methods\|options_m\|option" value="show" />
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	192 <param name="methods\|options_m\|max" value="50" />
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	193 <param name="methods\|options_m\|snthresh" value="1" />
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	194 <param name="methods\|options_m\|steps" value="2" />
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	195 <output name="log">
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	196 <assert_contents>
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	197 <has_text text="object with 4 samples" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	198 <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	199 <has_text text="Mass range: 50.0021-999.9863 m/z" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	200 <has_text text="Peaks: 59359 (about 14840 per sample)" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	201 <has_text text="Peak Groups: 0" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	202 <has_text text="Sample classes: bio, blank" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	203 </assert_contents>
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	204 </output>
10 00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	205 </test>
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	206 <test>
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	207 <param name="inputs\|input" value="zip_file" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	208 <param name="inputs\|zip_file" value="sacuri_current_root.zip" ftype="zip" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	209 <param name="methods\|method" value="centWave" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	210 <param name="methods\|ppm" value="25" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	211 <param name="methods\|peakwidth" value="20,50" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	212 <output name="log">
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	213 <assert_contents>
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	214 <has_text text="object with 4 samples" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	215 <has_text text="Time range: 3.5-1139.2 seconds (0.1-19 minutes)" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	216 <has_text text="Mass range: 57.9756-593.4086 m/z" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	217 <has_text text="Peaks: 1535 (about 384 per sample)" />
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	218 <has_text text="Peak Groups: 0" />
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	219 <has_text text="Sample classes: bio, blank" />
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	220 </assert_contents>
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	221 </output>
10 00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	222 </test>-->
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	223 <test>
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	224 <param name="inputs\|input" value="zip_file" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	225 <param name="inputs\|zip_file" value="faahKO_reduce.zip" ftype="zip" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	226 <param name="methods\|method" value="centWave" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	227 <param name="methods\|ppm" value="25" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	228 <param name="methods\|peakwidth" value="20,50" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	229 <output name="log">
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	230 <assert_contents>
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	231 <has_text text="object with 4 samples" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	232 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	233 <has_text text="Mass range: 200.1-600 m/z" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	234 <has_text text="Peaks: 9251 (about 2313 per sample)" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	235 <has_text text="Peak Groups: 0" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	236 <has_text text="Sample classes: KO, WT" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	237 </assert_contents>
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	238 </output>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	239 </test>
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	240 <!-- Passed by disable to save time for Travis"
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	241 <!--<test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	242 <param name="inputs\|input" value="single_file" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	243 <param name="inputs\|single_file" value="ko15.CDF" ftype="netcdf" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	244 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	245 <param name="methods\|ppm" value="25" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	246 <param name="methods\|peakwidth" value="20,50" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	247 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	248 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	249 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	250 <has_text text="Time range: 2506.1-4471.7 seconds (41.8-74.5 minutes)" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	251 <has_text text="Mass range: 200.2-600 m/z" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	252 <has_text text="Peaks: 2262 (about 2262 per sample)" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	253 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	254 <has_text text="Sample classes: ." />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	255 </assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	256 </output>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	257 </test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	258 <test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	259 <param name="inputs\|input" value="single_file" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	260 <param name="inputs\|single_file" value="ko16.CDF" ftype="netcdf" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	261 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	262 <param name="methods\|ppm" value="25" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	263 <param name="methods\|peakwidth" value="20,50" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	264 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	265 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	266 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	267 <has_text text="Time range: 2521.7-4477.9 seconds (42-74.6 minutes)" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	268 <has_text text="Mass range: 200.1-600 m/z" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	269 <has_text text="Peaks: 2408 (about 2408 per sample)" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	270 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	271 <has_text text="Sample classes: ." />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	272 </assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	273 </output>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	274 </test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	275 <test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	276 <param name="inputs\|input" value="single_file" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	277 <param name="inputs\|single_file" value="wt15.CDF" ftype="netcdf" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	278 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	279 <param name="methods\|ppm" value="25" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	280 <param name="methods\|peakwidth" value="20,50" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	281 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	282 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	283 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	284 <has_text text="Time range: 2517-4473.2 seconds (42-74.6 minutes)" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	285 <has_text text="Mass range: 200.2-599.8 m/z" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	286 <has_text text="Peaks: 2278 (about 2278 per sample)" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	287 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	288 <has_text text="Sample classes: ." />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	289 </assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	290 </output>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	291 </test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	292 <test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	293 <param name="inputs\|input" value="single_file" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	294 <param name="inputs\|single_file" value="wt16.CDF" ftype="netcdf" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	295 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	296 <param name="methods\|ppm" value="25" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	297 <param name="methods\|peakwidth" value="20,50" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	298 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	299 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	300 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	301 <has_text text="Time range: 2521.7-4468.5 seconds (42-74.5 minutes)" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	302 <has_text text="Mass range: 200.3-600 m/z" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	303 <has_text text="Peaks: 2303 (about 2303 per sample)" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	304 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	305 <has_text text="Sample classes: ." />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	306 </assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	307 </output>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	308 </test>-->
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	309 <test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	310 <param name="inputs\|input" value="single_file" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	311 <param name="inputs\|single_file" value="HU_neg_017.mzXML" ftype="mzxml" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	312 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	313 <param name="methods\|ppm" value="25" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	314 <param name="methods\|peakwidth" value="20,50" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	315 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	316 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	317 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	318 <has_text text="Time range: 3.5-1139.1 seconds (0.1-19 minutes)" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	319 <has_text text="Mass range: 57.9756-556.8128 m/z" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	320 <has_text text="Peaks: 380 (about 380 per sample)" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	321 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	322 <has_text text="Sample classes: ." />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	323 </assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	324 </output>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	325 </test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	326 <test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	327 <param name="inputs\|input" value="single_file" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	328 <param name="inputs\|single_file" value="MM14.mzML" ftype="mzxml" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	329 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	330 <param name="methods\|ppm" value="56" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	331 <param name="methods\|peakwidth" value="5.275,13.5" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	332 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	333 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	334 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	335 <has_text text="Time range: 271-307.3 seconds (4.5-5.1 minutes)" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	336 <has_text text="Mass range: 117.0357-936.7059 m/z" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	337 <has_text text="Peaks: 222 (about 222 per sample)" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	338 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	339 <has_text text="Sample classes: ." />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	340 </assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	341 </output>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	342 </test>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	343 </tests>
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	344
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	345 <help><![CDATA[
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	346
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	347 @HELP_AUTHORS@
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	348
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	349 ============
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	350 Xcms.xcmsSet
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	351 ============
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	352
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	353 -----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	354 Description
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	355 -----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	356
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	357 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.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	358 You can read a tutorial on how to perform xcms preprocessing which is available here_.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	359
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	360 .. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	361
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	362
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	363 -----------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	364 Workflow position
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	365 -----------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	366
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	367 Upstream tools
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	368
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	369 ========================= ================= ======= =========
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	370 Name output file format parameter
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	371 ========================= ================= ======= =========
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	372 NA NA zip NA
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	373 ========================= ================= ======= =========
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	374
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	375
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	376 Downstream tools
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	377
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	378 +---------------------------+--------------------+-----------------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	379 \| Name \| Output file \| Format \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	380 +===========================+====================+=================+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	381 \|xcms.group \| xset.RData \| rdata.xcms.raw \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	382 +---------------------------+--------------------+-----------------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	383 \|PCA ellipsoid by factors \| sampleMetadata.tsv \| Tabular \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	384 +---------------------------+--------------------+-----------------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	385 \|Anova \| sampleMetadata.tsv \| Tabular \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	386 +---------------------------+--------------------+-----------------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	387
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	388
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	389 Example of a metabolomic workflow
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	390
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	391 .. image:: XCMS_Galaxy_workflow.png
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	392
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	393
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	394 ------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	395
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	396 .. class:: infomark
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	397
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	398 The output file is an xset.RData file. You can continue your analysis using it in xcms.group tool.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	399
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	400 ---------------------------------------------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	401
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	402
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	403
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	404 -----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	405 Input files
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	406 -----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	407
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	408 +---------------------------+--------------------+
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	409 \| Parameter : num + label \| Format \|
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	410 +===========================+====================+
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	411 \| OR : Zip file \| zip \|
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	412 +---------------------------+--------------------+
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	413 \| OR : Single file \| mzXML, netCDF \|
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	414 +---------------------------+--------------------+
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	415
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	416 Choose your inputs
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	417
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	418 You have two methods for your inputs:
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	419
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	420 \| Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	421 \| Single file: 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"
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	422
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	423 Zip file: Steps for creating the zip file
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	424 -----------------------------------------
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	425
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	426 Step1: Creating your directory and hierarchize the subdirectories
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	427
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	428
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	429 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).
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	430
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	431 Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	432 arabidopsis/wild/01.raw
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	433 arabidopsis/mutant/01.raw
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	434
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	435 Step2: Creating a zip file
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	436
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	437 Create your zip file (e.g.: arabidopsis.zip).
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	438
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	439 Step 3 : Uploading it to our Galaxy server
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	440
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	441 If your zip file is less than 2Gb, you get use the Get Data tool to upload it.
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	442
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	443 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).
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	444
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	445 For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	446
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	447 Advices for converting your files for the XCMS input
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	448 ----------------------------------------------------
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	449
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	450 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.
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	451
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	452 We recommend you the following parameters:
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	453
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	454 Use Filtering: True
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	455
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	456 Use Peak Picking: True
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	457
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	458 Peak Peaking -Apply to MS Levels: All Levels (1-) : Centroid Mode
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	459
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	460 Use zlib: 64
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	461
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	462 Binary Encoding: 64
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	463
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	464 m/z Encoding: 64
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	465
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	466 Intensity Encoding: 64
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	467
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	468
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	469 ----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	470 Parameters
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	471 ----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	472
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	473 Extraction method for peaks detection
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	474 -------------------------------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	475
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	476 Matched Filter
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	477
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	478 \| One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm.
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	479 \| For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002).
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	480
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	481
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	482 cent Wave
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	483
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	484 \| This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	485 \| Due to the fact that peak centroids are used, a binning step is not necessary.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	486 \| 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.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	487
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	488 MSW
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	489
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	490 \| Wavelet based, used for direct infusion data. Continuous wavelet transform (CWT) can be used to locate chromatographic peaks on different scales.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	491 \| If you wish to have more details about the other parameters, you can read the following documents:
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	492 \| -Example of preprocessing data with XCMS : http://www.bioconductor.org/packages/2.12/bioc/vignettes/xcms/inst/doc/xcmsPreprocess.pdf
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	493 \| -Details and explanations for all the parameters of XCMS package: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	494
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	495
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	496 ------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	497 Output files
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	498 ------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	499
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	500 xset.TICs_raw.pdf
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	501
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	502 \| "Total Ion Chromatograms" graph in pdf format.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	503
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	504 xset.BPCs_raw.pdf
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	505
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	506 \| "Base Peak Chromatograms" graph in pdf format with each class samples opposed.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	507
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	508 sampleMetadata.tsv
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	509
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	510 \| Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed).
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	511 \| This file is necessary in the Anova and PCA step of the workflow.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	512
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	513 xset.RData: rdata.xcms.raw format
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	514
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	515 \| Rdata file that is necessary in the second step of the workflow "xcms.group".
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	516
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	517 ------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	518
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	519 .. class:: infomark
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	520
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	521 The output file is an xset.RData file. You can continue your analysis using it in xcms.group tool.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	522
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	523 ---------------------------------------------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	524
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	525 ---------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	526 Working example
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	527 ---------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	528
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	529 Input files
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	530 -----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	531
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	532 \| zip_file -> sacuri.zip
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	533
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	534 Parameters
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	535 ----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	536
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	537 \| Method -> matchedFilter
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	538 \| step -> 0.01
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	539 \| fwhm -> 4
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	540 \| Advanced option -> show
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	541 \| max: -> 50
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	542 \| snthresh -> 1
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	543 \| steps -> 2
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	544
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	545
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	546 Output files
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	547 ------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	548
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	549 \| 1) xset.RData: RData file
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	550
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	551 \| 2) Example of a sampleMetadata.tsv :
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	552
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	553
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	554 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	555 \| sampleMetadata \| class \| polarity\|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	556 +===========================+============+=========+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	557 \|HU_neg_017 \| bio \|negative \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	558 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	559 \|HU_neg_028 \| bio \|negative \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	560 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	561 \|HU_neg_034 \| bio \|negative \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	562 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	563 \|Blanc04 \| blank \|negative \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	564 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	565 \|Blanc06 \| blank \|negative \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	566 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	567 \|Blanc09 \| blank \|negative \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	568 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	569
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	570
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	571
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	572 \| 3) Example of xset.TICs_raw.pdf (Total Ion Chromatograms) :
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	573
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	574 .. image:: xcms_tics.png
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	575
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	576
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	577 ---------------------------------------------------
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	578
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	579 Changelog/News
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	580 --------------
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	581
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	582 Version 2.1.0 - 03/02/2017
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	583
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	584 - 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".
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	585
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	586 Version 2.0.11 - 22/12/2016
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	587
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	588 - BUGFIX: propose scanrange for all methods
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	589
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	590 Version 2.0.10 - 22/12/2016
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	591
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	592 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	593
13 68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 10 diff changeset	594 Version 2.0.9 - 06/07/2016
68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 10 diff changeset	595
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	596 - UPGRADE: upgrade the xcms version from 1.44.0 to 1.46.0
13 68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 10 diff changeset	597
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	598 Version 2.0.8 - 06/04/2016
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	599
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	600 - TEST: refactoring to pass planemo test using conda dependencies
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	601
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	602
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	603 Version 2.0.7 - 10/02/2016
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	604
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	605 - BUGFIX: better management of errors. Datasets remained green although the process failed
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	606
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	607 - 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
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	608
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	609 - BUGFIX/IMPROVEMENT: New step to check and delete bad characters in the XML: accented characters in the storage path of the mass spectrometer
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	610
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	611 - UPDATE: refactoring of internal management of inputs/outputs
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	612
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	613 - TEST: refactoring to feed the new report tool
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	614
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	615
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	616 **Version 2.0.2 - 18/01/2016
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	617
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	618 - BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	619
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	620
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	621 Version 2.0.2 - 09/10/2015
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	622
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	623 - 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.
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	624
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	625
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	626 Version 2.0.2 - 02/06/2015
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	627
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	628 - 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.
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	629
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	630 - 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.
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	631
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	632 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	633
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	634 ]]></help>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	635
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	636 <expand macro="citation" />
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	637 </tool>

Mercurial > repos > lecorguille > xcms_xcmsset

annotate abims_xcms_xcmsSet.xml @ 17:602acc32b549 draft