xcms_xcmsset: abims_xcms_xcmsSet.xml annotate

annotate abims_xcms_xcmsSet.xml @ 26:626d3db664ef draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf

author	lecorguille
date	Wed, 22 Mar 2017 16:04:45 -0400
parents	dc4d3e2b9968
children	b90e4f92e8b5

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
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	14 #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"):
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	15 singlefile_galaxyPath '$input' singlefile_sampleName '$input.name'
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	16 #else
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	17 zipfile '$input'
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
23 329cfa3d2be6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4 lecorguille parents: 20 diff changeset	22 xsetRdataOutput '$xsetRData'
329cfa3d2be6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4 lecorguille parents: 20 diff changeset	23 sampleMetadataOutput '$sampleMetadata'
329cfa3d2be6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4 lecorguille parents: 20 diff changeset	24 ticspdf '$ticsRawPdf'
329cfa3d2be6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4 lecorguille parents: 20 diff changeset	25 bicspdf '$bpcsRawPdf'
1 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 steps $methods.options_m.steps
26 626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 25 diff changeset	52 mzdiff $methods.options_m.mzdiff
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	53 #end if
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	54 #elif $methods.method == "MSW":
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	55 snthr $methods.snthr
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	56 nearbyPeak $methods.nearbyPeak
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	57 winSize.noise $methods.winSize_noise
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	58 amp.Th $methods.amp_Th
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	59 scales "c($methods.scales)"
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	60 SNR.method "$methods.SNR_method"
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	61 #end if
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	62 @COMMAND_LOG_EXIT@
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	63 ]]></command>
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	64
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	65 <inputs>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	66
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 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 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	68
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	69 <conditional name="options_scanrange">
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	70 <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	71 <option value="show">show</option>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	72 <option value="hide" selected="true">hide</option>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	73 </param>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	74 <when value="show">
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	75 <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	76 <validator type="empty_field"/>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	77 </param>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	78 </when>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	79 <when value="hide">
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	80 </when>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	81 </conditional>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	82
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	83
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	84 <!--
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	85 <param name="profmethod" type="select" label="Method to use for profile generation (profmethod)" >
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	86 <option value="bin" selected="true">bin</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	87 <option value="binlin">binlin</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	88 <option value="binlinbase">binlinbase</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	89 <option value="intlin">intlin</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	90 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	91 -->
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	92 <conditional name="methods">
1bad16e5e4ae 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">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	94 <option value="centWave" >centWave</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	95 <option value="matchedFilter" selected="true">matchedFilter</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	96 <option value="MSW">MSW</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	97 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	98
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	99 <!-- centWave Filter options -->
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	100 <when value="centWave">
1bad16e5e4ae 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]" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	102 <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	103
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	104 <conditional name="options_c">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	105 <param name="option" type="select" label="Advanced options" >
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	106 <option value="show">show</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	107 <option value="hide" selected="true">hide</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	108 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	109 <when value="show">
1bad16e5e4ae 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" />
26 626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 25 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 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	112 <param name="integrate" type="select" label="peak limits method" help="[integrate]" >
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	113 <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	114 <option value="2">peak limits based on real data (more sensitive to noise)</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	115 </param>
1bad16e5e4ae 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’"/>
1bad16e5e4ae 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"/>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	118 </when>
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	119 <when value="hide">
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	120 </when>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	121 </conditional>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	122 </when>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	123
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	124 <!-- matched Filter options -->
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	125 <when value="matchedFilter">
26 626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 25 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 1bad16e5e4ae 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" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	128 <conditional name="options_m">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	129 <param name="option" type="select" label="Advanced options" >
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	130 <option value="show">show</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	131 <option value="hide" selected="true">hide</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	132 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	133 <when value="show">
26 626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 25 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 1bad16e5e4ae 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]" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	136 <param name="snthresh" type="integer" value="10" label="Signal to noise ratio cutoff" help="[snthresh]" />
1bad16e5e4ae 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" />
26 626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 25 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 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	139 </when>
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	140 <when value="hide">
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	141 </when>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	142 </conditional>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	143 </when>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	144
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	145 <!-- MSW Filter options -->
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	146 <when value="MSW">
1bad16e5e4ae 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]" >
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	148 <option value="TRUE">TRUE</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	149 <option value="FALSE">FALSE</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	150 </param>
1bad16e5e4ae 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]" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	152 <param name="snthr" type="integer" value="3" label="SNR (Signal to Noise Ratio) threshold" help="[snthr]" />
1bad16e5e4ae 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" />
1bad16e5e4ae 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 " />
1bad16e5e4ae 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." />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	156 </when>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	157 </conditional>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	158 </inputs>
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	159
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	160 <outputs>
25 dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	161 <data name="xsetRData" format="rdata.xcms.raw" label="${input.name.rsplit('.',1)[0]}.xset.RData" />
dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	162 <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv">
dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	163 <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	164 </data>
dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	165 <data name="ticsRawPdf" format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.pdf" />
dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	166 <data name="bpcsRawPdf" format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.pdf" />
dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	167 <data name="log" format="txt" label="${input.name.rsplit('.',1)[0]}.xset.log.txt" />
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	168 </outputs>
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	169
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	170 <tests>
10 00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	171 <!--<test>
25 dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	172 <param name="input" value="sacuri_dir_root.zip" ftype="zip" />
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	173 <param name="methods\|method" value="matchedFilter" />
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	174 <param name="methods\|step" value="0.01" />
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	175 <param name="methods\|fwhm" value="4" />
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	176 <param name="methods\|options_m\|option" value="show" />
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	177 <param name="methods\|options_m\|max" value="50" />
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	178 <param name="methods\|options_m\|snthresh" value="1" />
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	179 <param name="methods\|options_m\|steps" value="2" />
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	180 <output name="log">
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	181 <assert_contents>
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	182 <has_text text="object with 4 samples" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	183 <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	184 <has_text text="Mass range: 50.0021-999.9863 m/z" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	185 <has_text text="Peaks: 59359 (about 14840 per sample)" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	186 <has_text text="Peak Groups: 0" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	187 <has_text text="Sample classes: bio, blank" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	188 </assert_contents>
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	189 </output>
10 00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	190 </test>
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	191 <test>
25 dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	192 <param name="input" value="sacuri_current_root.zip" ftype="zip" />
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	193 <param name="methods\|method" value="centWave" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	194 <param name="methods\|ppm" value="25" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	195 <param name="methods\|peakwidth" value="20,50" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	196 <output name="log">
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	197 <assert_contents>
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	198 <has_text text="object with 4 samples" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	199 <has_text text="Time range: 3.5-1139.2 seconds (0.1-19 minutes)" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	200 <has_text text="Mass range: 57.9756-593.4086 m/z" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	201 <has_text text="Peaks: 1535 (about 384 per sample)" />
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	202 <has_text text="Peak Groups: 0" />
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	203 <has_text text="Sample classes: bio, blank" />
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	204 </assert_contents>
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	205 </output>
10 00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	206 </test>-->
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	207 <test>
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	208 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
10 00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	209 <param name="methods\|method" value="centWave" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	210 <param name="methods\|ppm" value="25" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	211 <param name="methods\|peakwidth" value="20,50" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	212 <output name="log">
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	213 <assert_contents>
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	214 <has_text text="object with 4 samples" />
00ef27ba8abd 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)" />
00ef27ba8abd 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" />
00ef27ba8abd 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)" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	218 <has_text text="Peak Groups: 0" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	219 <has_text text="Sample classes: KO, WT" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	220 </assert_contents>
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	221 </output>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	222 </test>
20 d7971ea3ad1d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 717c02f887ce343ca55f862c8020aaf49f5581d8 lecorguille parents: 17 diff changeset	223 <!-- Passed but disable to save time for Travis" -->
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	224 <!--<test>
25 dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	225 <param name="input" value="ko15.CDF" ftype="netcdf" />
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	226 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	227 <param name="methods\|ppm" value="25" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	228 <param name="methods\|peakwidth" value="20,50" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	229 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	230 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	231 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	232 <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	233 <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	234 <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	235 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	236 <has_text text="Sample classes: ." />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	237 </assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	238 </output>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	239 </test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	240 <test>
25 dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	241 <param name="input" value="ko16.CDF" ftype="netcdf" />
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	242 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	243 <param name="methods\|ppm" value="25" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	244 <param name="methods\|peakwidth" value="20,50" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	245 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	246 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	247 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	248 <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	249 <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	250 <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	251 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	252 <has_text text="Sample classes: ." />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	253 </assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	254 </output>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	255 </test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	256 <test>
25 dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	257 <param name="input" value="wt15.CDF" ftype="netcdf" />
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	258 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	259 <param name="methods\|ppm" value="25" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	260 <param name="methods\|peakwidth" value="20,50" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	261 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	262 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	263 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	264 <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	265 <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	266 <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	267 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	268 <has_text text="Sample classes: ." />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	269 </assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	270 </output>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	271 </test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	272 <test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	273 <param name="inputs\|input" value="single_file" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	274 <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	275 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	276 <param name="methods\|ppm" value="25" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	277 <param name="methods\|peakwidth" value="20,50" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	278 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	279 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	280 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	281 <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	282 <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	283 <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	284 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	285 <has_text text="Sample classes: ." />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	286 </assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	287 </output>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	288 </test>-->
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	289 <test>
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	290 <param name="input" value="HU_neg_017.mzXML" ftype="mzxml" />
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	291 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	292 <param name="methods\|ppm" value="25" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	293 <param name="methods\|peakwidth" value="20,50" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	294 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	295 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	296 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	297 <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	298 <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	299 <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	300 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	301 <has_text text="Sample classes: ." />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	302 </assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	303 </output>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	304 </test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	305 <test>
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	306 <param name="input" value="MM14.mzML" ftype="mzxml" />
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	307 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	308 <param name="methods\|ppm" value="56" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	309 <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	310 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	311 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	312 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	313 <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	314 <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	315 <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	316 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	317 <has_text text="Sample classes: ." />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	318 </assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	319 </output>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	320 </test>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	321 </tests>
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	322
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	323 <help><![CDATA[
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	324
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	325 @HELP_AUTHORS@
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	326
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	327 ============
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	328 Xcms.xcmsSet
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	329 ============
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	330
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	331 -----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	332 Description
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	333 -----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	334
1bad16e5e4ae 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.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	336 You can read a tutorial on how to perform xcms preprocessing which is available here_.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	337
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	338 .. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	339
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	340
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	341 -----------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	342 Workflow position
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	343 -----------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	344
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	345 Upstream tools
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	346
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	347 ========================= ================= ======= =========
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	348 Name output file format parameter
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	349 ========================= ================= ======= =========
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	350 NA NA zip NA
0 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 Downstream tools
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	355
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	356 +---------------------------+--------------------+-----------------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	357 \| Name \| Output file \| Format \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	358 +===========================+====================+=================+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	359 \|xcms.group \| xset.RData \| rdata.xcms.raw \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	360 +---------------------------+--------------------+-----------------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	361 \|PCA ellipsoid by factors \| sampleMetadata.tsv \| Tabular \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	362 +---------------------------+--------------------+-----------------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	363 \|Anova \| sampleMetadata.tsv \| Tabular \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	364 +---------------------------+--------------------+-----------------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	365
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	366
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	367 Example of a metabolomic workflow
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	368
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	369 .. image:: XCMS_Galaxy_workflow.png
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	370
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	371
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	372 ------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	373
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	374 .. class:: infomark
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	375
1bad16e5e4ae 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.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	377
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	378 ---------------------------------------------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	379
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	380
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	381
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	382 -----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	383 Input files
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	384 -----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	385
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	386 +---------------------------+----------------------------------+
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	387 \| Parameter : num + label \| Format \|
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	388 +===========================+==================================+
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	389 \| OR : Zip file \| zip \|
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	390 +---------------------------+----------------------------------+
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	391 \| OR : Single file \| mzXML, mzML, mzData, netCDF \|
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	392 +---------------------------+----------------------------------+
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	393
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	394 Choose your inputs
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	395
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	396 You have two methods for your inputs:
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	397
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 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"
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	399 \| Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	400
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	401 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	402 -----------------------------------------
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	403
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	404 Step1: Creating your directory and hierarchize the subdirectories
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	405
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	406
4509e9dd03e4 planemo upload lecorguille parents: 3 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).
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	408
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	409 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	410 arabidopsis/wild/01.raw
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	411 arabidopsis/mutant/01.raw
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	412
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	413 Step2: Creating a zip file
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	414
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	415 Create your zip file (e.g.: arabidopsis.zip).
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	416
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	417 Step 3 : Uploading it to our Galaxy server
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	418
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	419 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	420
4509e9dd03e4 planemo upload lecorguille parents: 3 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).
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	422
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	423 For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	424
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	425 Advices for converting your files for the XCMS input
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	426 ----------------------------------------------------
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	427
4509e9dd03e4 planemo upload lecorguille parents: 3 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.
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	429
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	430 We recommend you the following parameters:
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	431
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	432 Use Filtering: True
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	433
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	434 Use Peak Picking: True
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	435
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	436 Peak Peaking -Apply to MS Levels: All Levels (1-) : Centroid Mode
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	437
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	438 Use zlib: 64
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	439
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	440 Binary Encoding: 64
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	441
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	442 m/z Encoding: 64
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	443
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	444 Intensity Encoding: 64
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	445
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	446
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	447 ----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	448 Parameters
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	449 ----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	450
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	451 Extraction method for peaks detection
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	452 -------------------------------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	453
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	454 Matched Filter
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	455
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 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 1bad16e5e4ae 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).
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	458
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	459
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	460 cent Wave
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	461
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	462 \| This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	463 \| Due to the fact that peak centroids are used, a binning step is not necessary.
1bad16e5e4ae 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.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	465
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	466 MSW
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	467
1bad16e5e4ae 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.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	469 \| If you wish to have more details about the other parameters, you can read the following documents:
1bad16e5e4ae 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
1bad16e5e4ae 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
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	472
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	473
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	474 ------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	475 Output files
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	476 ------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	477
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	478 xset.TICs_raw.pdf
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	479
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	480 \| "Total Ion Chromatograms" graph in pdf format.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	481
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	482 xset.BPCs_raw.pdf
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	483
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	484 \| "Base Peak Chromatograms" graph in pdf format with each class samples opposed.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	485
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	486 sampleMetadata.tsv
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	487
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	488 \| Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed).
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	489 \| This file is necessary in the Anova and PCA step of the workflow.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	490
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	491 xset.RData: rdata.xcms.raw format
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	492
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	493 \| 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	494
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	495 ------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	496
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	497 .. class:: infomark
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	498
1bad16e5e4ae 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.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	500
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	501 ---------------------------------------------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	502
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	503 ---------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	504 Working example
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	505 ---------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	506
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	507 Input files
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	508 -----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	509
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	510 \| zip_file -> sacuri.zip
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	511
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	512 Parameters
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	513 ----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	514
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	515 \| Method -> matchedFilter
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	516 \| step -> 0.01
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	517 \| fwhm -> 4
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	518 \| Advanced option -> show
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	519 \| max: -> 50
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	520 \| snthresh -> 1
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	521 \| steps -> 2
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	522
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	523
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	524 Output files
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	525 ------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	526
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	527 \| 1) xset.RData: RData file
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	528
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	529 \| 2) Example of a sampleMetadata.tsv :
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	530
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	531
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	532 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	533 \| sampleMetadata \| class \| polarity\|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	534 +===========================+============+=========+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	535 \|HU_neg_017 \| bio \|negative \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	536 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	537 \|HU_neg_028 \| bio \|negative \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	538 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	539 \|HU_neg_034 \| bio \|negative \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	540 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	541 \|Blanc04 \| blank \|negative \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	542 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	543 \|Blanc06 \| blank \|negative \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	544 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	545 \|Blanc09 \| blank \|negative \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	546 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	547
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	548
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	549
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	550 \| 3) Example of xset.TICs_raw.pdf (Total Ion Chromatograms) :
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	551
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	552 .. image:: xcms_tics.png
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	553
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	554
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	555 ---------------------------------------------------
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	556
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	557 Changelog/News
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	558 --------------
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	559
26 626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 25 diff changeset	560 Version 2.1.0 - 22/02/2017
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	561
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	562 - 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	563
26 626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 25 diff changeset	564 - 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
626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 25 diff changeset	565
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	566 Version 2.0.11 - 22/12/2016
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	567
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	568 - BUGFIX: propose scanrange for all methods
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	569
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	570 Version 2.0.10 - 22/12/2016
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	571
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	572 - 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	573
13 68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 10 diff changeset	574 Version 2.0.9 - 06/07/2016
68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 10 diff changeset	575
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	576 - 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	577
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	578 Version 2.0.8 - 06/04/2016
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	579
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	580 - TEST: refactoring to pass planemo test using conda dependencies
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	581
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	582
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	583 Version 2.0.7 - 10/02/2016
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	584
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	585 - BUGFIX: better management of errors. Datasets remained green although the process failed
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	586
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	587 - 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	588
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	589 - 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	590
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	591 - UPDATE: refactoring of internal management of inputs/outputs
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	592
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	593 - TEST: refactoring to feed the new report tool
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	594
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	595
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	596 **Version 2.0.2 - 18/01/2016
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	597
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	598 - 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	599
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	600
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	601 Version 2.0.2 - 09/10/2015
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	602
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	603 - 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	604
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	605
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	606 Version 2.0.2 - 02/06/2015
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	607
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	608 - 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	609
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	610 - 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	611
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	612 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	613
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	614 ]]></help>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	615
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	616 <expand macro="citation" />
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	617 </tool>

Mercurial > repos > lecorguille > xcms_xcmsset

annotate abims_xcms_xcmsSet.xml @ 26:626d3db664ef draft