xcms_xcmsset: abims_xcms_xcmsSet.xml annotate

annotate abims_xcms_xcmsSet.xml @ 25:dc4d3e2b9968 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312

author	lecorguille
date	Thu, 02 Mar 2017 08:20:04 -0500
parents	d8915395681f
children	626d3db664ef

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 ## 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
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	68 <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	69
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	70 <conditional name="options_scanrange">
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	71 <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	72 <option value="show">show</option>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	73 <option value="hide" selected="true">hide</option>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	74 </param>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	75 <when value="show">
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	76 <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	77 <validator type="empty_field"/>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	78 </param>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	79 </when>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	80 <when value="hide">
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	81 </when>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	82 </conditional>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	83
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	84
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	85 <!--
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	86 <param name="profmethod" type="select" label="Method to use for profile generation (profmethod)" >
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	87 <option value="bin" selected="true">bin</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	88 <option value="binlin">binlin</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	89 <option value="binlinbase">binlinbase</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	90 <option value="intlin">intlin</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	91 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	92 -->
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	93 <conditional name="methods">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	94 <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	95 <option value="centWave" >centWave</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	96 <option value="matchedFilter" selected="true">matchedFilter</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	97 <option value="MSW">MSW</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	98 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	99
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	100 <!-- centWave Filter options -->
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	101 <when value="centWave">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	102 <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	103 <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	104
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	105 <conditional name="options_c">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	106 <param name="option" type="select" label="Advanced options" >
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	107 <option value="show">show</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	108 <option value="hide" selected="true">hide</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	109 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	110 <when value="show">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	111 <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	112 <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	113 <param name="integrate" type="select" label="peak limits method" help="[integrate]" >
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	114 <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	115 <option value="2">peak limits based on real data (more sensitive to noise)</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	116 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	117 <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	118 <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	119 </when>
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	120 <when value="hide">
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	121 </when>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	122 </conditional>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	123 </when>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	124
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	125 <!-- matched Filter options -->
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	126 <when value="matchedFilter">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	127 <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	128 <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	129 <conditional name="options_m">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	130 <param name="option" type="select" label="Advanced options" >
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	131 <option value="show">show</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	132 <option value="hide" selected="true">hide</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	133 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	134 <when value="show">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	135 <!--
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	136 <param name="sigma" type="hidden" value="fwhm/2.3548" label="sigma" help="standard deviation (fwhm/2.3548)" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	137 -->
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	138 <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	139 <param name="snthresh" type="integer" value="10" label="Signal to noise ratio cutoff" help="[snthresh]" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	140 <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	141 <!--
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	142 <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	143 -->
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	144 </when>
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	145 <when value="hide">
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	146 </when>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	147 </conditional>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	148 </when>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	149
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	150 <!-- MSW Filter options -->
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	151 <when value="MSW">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	152 <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	153 <option value="TRUE">TRUE</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	154 <option value="FALSE">FALSE</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	155 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	156 <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	157 <param name="snthr" type="integer" value="3" label="SNR (Signal to Noise Ratio) threshold" help="[snthr]" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	158 <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	159 <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	160 <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	161 </when>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	162 </conditional>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	163 </inputs>
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	164
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	165 <outputs>
25 dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	166 <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	167 <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv">
dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	168 <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	169 </data>
dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	170 <data name="ticsRawPdf" format="pdf" label="${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	171 <data name="bpcsRawPdf" format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.pdf" />
dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	172 <data name="log" format="txt" label="${input.name.rsplit('.',1)[0]}.xset.log.txt" />
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	173 </outputs>
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	174
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	175 <tests>
10 00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	176 <!--<test>
25 dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	177 <param name="input" value="sacuri_dir_root.zip" ftype="zip" />
5 b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	178 <param name="methods\|method" value="matchedFilter" />
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	179 <param name="methods\|step" value="0.01" />
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	180 <param name="methods\|fwhm" value="4" />
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	181 <param name="methods\|options_m\|option" value="show" />
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	182 <param name="methods\|options_m\|max" value="50" />
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	183 <param name="methods\|options_m\|snthresh" value="1" />
b9a87af62223 planemo upload commit 5a5b747865d7fb76f711bce2d9ce2a0f82a2a374-dirty lecorguille parents: 4 diff changeset	184 <param name="methods\|options_m\|steps" value="2" />
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	185 <output name="log">
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	186 <assert_contents>
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	187 <has_text text="object with 4 samples" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	188 <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	189 <has_text text="Mass range: 50.0021-999.9863 m/z" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	190 <has_text text="Peaks: 59359 (about 14840 per sample)" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	191 <has_text text="Peak Groups: 0" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	192 <has_text text="Sample classes: bio, blank" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	193 </assert_contents>
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	194 </output>
10 00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	195 </test>
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	196 <test>
25 dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	197 <param name="input" value="sacuri_current_root.zip" ftype="zip" />
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	198 <param name="methods\|method" value="centWave" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	199 <param name="methods\|ppm" value="25" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	200 <param name="methods\|peakwidth" value="20,50" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	201 <output name="log">
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	202 <assert_contents>
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	203 <has_text text="object with 4 samples" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	204 <has_text text="Time range: 3.5-1139.2 seconds (0.1-19 minutes)" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	205 <has_text text="Mass range: 57.9756-593.4086 m/z" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	206 <has_text text="Peaks: 1535 (about 384 per sample)" />
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	207 <has_text text="Peak Groups: 0" />
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	208 <has_text text="Sample classes: bio, blank" />
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	209 </assert_contents>
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	210 </output>
10 00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	211 </test>-->
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	212 <test>
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	213 <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	214 <param name="methods\|method" value="centWave" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	215 <param name="methods\|ppm" value="25" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	216 <param name="methods\|peakwidth" value="20,50" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	217 <output name="log">
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	218 <assert_contents>
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	219 <has_text text="object with 4 samples" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	220 <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	221 <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	222 <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	223 <has_text text="Peak Groups: 0" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	224 <has_text text="Sample classes: KO, WT" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	225 </assert_contents>
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	226 </output>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	227 </test>
20 d7971ea3ad1d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 717c02f887ce343ca55f862c8020aaf49f5581d8 lecorguille parents: 17 diff changeset	228 <!-- 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	229 <!--<test>
25 dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	230 <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	231 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	232 <param name="methods\|ppm" value="25" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	233 <param name="methods\|peakwidth" value="20,50" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	234 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	235 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	236 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	237 <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	238 <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	239 <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	240 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	241 <has_text text="Sample classes: ." />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	242 </assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	243 </output>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	244 </test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	245 <test>
25 dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	246 <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	247 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	248 <param name="methods\|ppm" value="25" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	249 <param name="methods\|peakwidth" value="20,50" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	250 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	251 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	252 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	253 <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	254 <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	255 <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	256 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	257 <has_text text="Sample classes: ." />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	258 </assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	259 </output>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	260 </test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	261 <test>
25 dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	262 <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	263 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	264 <param name="methods\|ppm" value="25" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	265 <param name="methods\|peakwidth" value="20,50" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	266 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	267 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	268 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	269 <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	270 <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	271 <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	272 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	273 <has_text text="Sample classes: ." />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	274 </assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	275 </output>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	276 </test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	277 <test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	278 <param name="inputs\|input" value="single_file" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	279 <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	280 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	281 <param name="methods\|ppm" value="25" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	282 <param name="methods\|peakwidth" value="20,50" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	283 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	284 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	285 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	286 <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	287 <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	288 <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	289 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	290 <has_text text="Sample classes: ." />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	291 </assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	292 </output>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	293 </test>-->
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	294 <test>
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	295 <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	296 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	297 <param name="methods\|ppm" value="25" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	298 <param name="methods\|peakwidth" value="20,50" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	299 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	300 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	301 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	302 <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	303 <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	304 <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	305 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	306 <has_text text="Sample classes: ." />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	307 </assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	308 </output>
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 <test>
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	311 <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	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="56" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	314 <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	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: 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	319 <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	320 <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	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>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	326 </tests>
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	327
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	328 <help><![CDATA[
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	329
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	330 @HELP_AUTHORS@
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	331
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	332 ============
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	333 Xcms.xcmsSet
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	334 ============
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	335
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	336 -----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	337 Description
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	338 -----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	339
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	340 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	341 You can read a tutorial on how to perform xcms preprocessing which is available here_.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	342
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	343 .. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	344
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	345
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	346 -----------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	347 Workflow position
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	348 -----------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	349
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	350 Upstream tools
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	351
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	352 ========================= ================= ======= =========
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	353 Name output file format parameter
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	354 ========================= ================= ======= =========
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	355 NA NA zip NA
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	356 ========================= ================= ======= =========
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	357
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	358
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	359 Downstream tools
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	360
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	361 +---------------------------+--------------------+-----------------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	362 \| Name \| Output file \| Format \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	363 +===========================+====================+=================+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	364 \|xcms.group \| xset.RData \| rdata.xcms.raw \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	365 +---------------------------+--------------------+-----------------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	366 \|PCA ellipsoid by factors \| sampleMetadata.tsv \| Tabular \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	367 +---------------------------+--------------------+-----------------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	368 \|Anova \| sampleMetadata.tsv \| Tabular \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	369 +---------------------------+--------------------+-----------------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	370
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	371
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	372 Example of a metabolomic workflow
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	373
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	374 .. image:: XCMS_Galaxy_workflow.png
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	375
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	376
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	377 ------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	378
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	379 .. class:: infomark
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	380
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	381 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	382
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	383 ---------------------------------------------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	384
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	385
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	386
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	387 -----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	388 Input files
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	389 -----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	390
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	391 +---------------------------+----------------------------------+
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	392 \| Parameter : num + label \| Format \|
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	393 +===========================+==================================+
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	394 \| OR : Zip file \| zip \|
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	395 +---------------------------+----------------------------------+
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	396 \| OR : Single file \| mzXML, mzML, mzData, netCDF \|
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	397 +---------------------------+----------------------------------+
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	398
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	399 Choose your inputs
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	400
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	401 You have two methods for your inputs:
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	402
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	403 \| 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	404 \| 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	405
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	406 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	407 -----------------------------------------
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	408
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	409 Step1: Creating your directory and hierarchize the subdirectories
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	410
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	411
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	412 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	413
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	414 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	415 arabidopsis/wild/01.raw
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	416 arabidopsis/mutant/01.raw
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	417
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	418 Step2: Creating a zip file
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	419
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	420 Create your zip file (e.g.: arabidopsis.zip).
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	421
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	422 Step 3 : Uploading it to our Galaxy server
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	423
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	424 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	425
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	426 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	427
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	428 For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	429
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	430 Advices for converting your files for the XCMS input
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	431 ----------------------------------------------------
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	432
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	433 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	434
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	435 We recommend you the following parameters:
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	436
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	437 Use Filtering: True
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	438
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	439 Use Peak Picking: True
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	440
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	441 Peak Peaking -Apply to MS Levels: All Levels (1-) : Centroid Mode
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	442
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	443 Use zlib: 64
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	444
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	445 Binary Encoding: 64
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	446
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	447 m/z Encoding: 64
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	448
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	449 Intensity Encoding: 64
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	450
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	451
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	452 ----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	453 Parameters
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	454 ----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	455
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	456 Extraction method for peaks detection
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	457 -------------------------------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	458
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	459 Matched Filter
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	460
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	461 \| 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	462 \| 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	463
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	464
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	465 cent Wave
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	466
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	467 \| This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	468 \| Due to the fact that peak centroids are used, a binning step is not necessary.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	469 \| 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	470
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	471 MSW
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	472
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	473 \| 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	474 \| If you wish to have more details about the other parameters, you can read the following documents:
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	475 \| -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	476 \| -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	477
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	478
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	479 ------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	480 Output files
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	481 ------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	482
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	483 xset.TICs_raw.pdf
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	484
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	485 \| "Total Ion Chromatograms" graph in pdf format.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	486
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	487 xset.BPCs_raw.pdf
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	488
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	489 \| "Base Peak Chromatograms" graph in pdf format with each class samples opposed.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	490
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	491 sampleMetadata.tsv
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	492
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	493 \| Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed).
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	494 \| This file is necessary in the Anova and PCA step of the workflow.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	495
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	496 xset.RData: rdata.xcms.raw format
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	497
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	498 \| 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	499
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	500 ------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	501
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	502 .. class:: infomark
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	503
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	504 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	505
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	506 ---------------------------------------------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	507
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	508 ---------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	509 Working example
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	510 ---------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	511
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	512 Input files
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	513 -----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	514
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	515 \| zip_file -> sacuri.zip
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	516
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	517 Parameters
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	518 ----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	519
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	520 \| Method -> matchedFilter
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	521 \| step -> 0.01
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	522 \| fwhm -> 4
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	523 \| Advanced option -> show
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	524 \| max: -> 50
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	525 \| snthresh -> 1
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	526 \| steps -> 2
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	527
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	528
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	529 Output 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 \| 1) xset.RData: RData file
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	533
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	534 \| 2) Example of a sampleMetadata.tsv :
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	535
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	536
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	537 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	538 \| sampleMetadata \| class \| polarity\|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	539 +===========================+============+=========+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	540 \|HU_neg_017 \| bio \|negative \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	541 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	542 \|HU_neg_028 \| bio \|negative \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	543 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	544 \|HU_neg_034 \| bio \|negative \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	545 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	546 \|Blanc04 \| blank \|negative \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	547 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	548 \|Blanc06 \| blank \|negative \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	549 +---------------------------+------------+---------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	550 \|Blanc09 \| blank \|negative \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	551 +---------------------------+------------+---------+
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 \| 3) Example of xset.TICs_raw.pdf (Total Ion Chromatograms) :
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	556
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	557 .. image:: xcms_tics.png
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	558
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	559
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	560 ---------------------------------------------------
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	561
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	562 Changelog/News
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	563 --------------
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	564
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	565 Version 2.1.0 - 03/02/2017
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	566
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	567 - 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	568
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	569 Version 2.0.11 - 22/12/2016
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	570
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	571 - BUGFIX: propose scanrange for all methods
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	572
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	573 Version 2.0.10 - 22/12/2016
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	574
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	575 - 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	576
13 68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 10 diff changeset	577 Version 2.0.9 - 06/07/2016
68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 10 diff changeset	578
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	579 - 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	580
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	581 Version 2.0.8 - 06/04/2016
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	582
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	583 - TEST: refactoring to pass planemo test using conda dependencies
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	584
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	585
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	586 Version 2.0.7 - 10/02/2016
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	587
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	588 - BUGFIX: better management of errors. Datasets remained green although the process failed
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	589
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	590 - 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	591
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	592 - 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	593
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	594 - UPDATE: refactoring of internal management of inputs/outputs
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	595
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	596 - TEST: refactoring to feed the new report tool
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	597
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	598
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	599 **Version 2.0.2 - 18/01/2016
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	600
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	601 - 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	602
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	603
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	604 Version 2.0.2 - 09/10/2015
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	605
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	606 - 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	607
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	608
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	609 Version 2.0.2 - 02/06/2015
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	610
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	611 - 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	612
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	613 - 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	614
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	615 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	616
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	617 ]]></help>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	618
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	619 <expand macro="citation" />
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	620 </tool>

Mercurial > repos > lecorguille > xcms_xcmsset

annotate abims_xcms_xcmsSet.xml @ 25:dc4d3e2b9968 draft