xcms_xcmsset: abims_xcms_xcmsSet.xml annotate

annotate abims_xcms_xcmsSet.xml @ 29:5dba1c94fb94 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9

author	lecorguille
date	Tue, 24 Oct 2017 11:46:21 -0400
parents	b90e4f92e8b5
children	d71827ecd22c

rev	line source
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	1 <tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.2.0">
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'
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	24
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	25 #if $options_scanrange.option == "show":
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	26 scanrange "c($options_scanrange.scanrange)"
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	27 #end if
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	28
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	29 ## profmethod $profmethod
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	30 nSlaves \${GALAXY_SLOTS:-1} method $methods.method
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	31 #if $methods.method == "centWave":
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	32 ppm $methods.ppm
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	33 peakwidth "c($methods.peakwidth)"
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	34 #if $methods.options_c.option == "show":
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	35 mzdiff $methods.options_c.mzdiff
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	36 snthresh $methods.options_c.snthresh
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	37 integrate $methods.options_c.integrate
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	38 noise $methods.options_c.noise
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	39 prefilter "c($methods.options_c.prefilter)"
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	40 #end if
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	41 #elif $methods.method == "matchedFilter":
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	42 step $methods.step
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	43 fwhm $methods.fwhm
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	44 #if $methods.options_m.option == "show":
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	45 ## sigma "$methods.options_m.sigma"
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	46 max $methods.options_m.max
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	47 snthresh $methods.options_m.snthresh
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	48 steps $methods.options_m.steps
26 626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 25 diff changeset	49 mzdiff $methods.options_m.mzdiff
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	50 #end if
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	51 #elif $methods.method == "MSW":
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	52 snthr $methods.snthr
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	53 nearbyPeak $methods.nearbyPeak
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	54 winSize.noise $methods.winSize_noise
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	55 amp.Th $methods.amp_Th
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	56 scales "c($methods.scales)"
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	57 SNR.method "$methods.SNR_method"
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	58 #end if
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	59
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	60 #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"):
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	61 && mv *-TIC_mqc.out $ticsRawTab
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	62 && mv *-BPC_mqc.out $bpcsRawTab
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	63 #end if
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	64
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	65 @COMMAND_LOG_EXIT@;
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	66 ]]></command>
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	67
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	68 <inputs>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	69
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	70 <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	71
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	72 <conditional name="options_scanrange">
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	73 <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	74 <option value="show">show</option>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	75 <option value="hide" selected="true">hide</option>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	76 </param>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	77 <when value="show">
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	78 <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	79 <validator type="empty_field"/>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	80 </param>
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 <when value="hide">
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	83 </when>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	84 </conditional>
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	85
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	86
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	87 <!--
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	88 <param name="profmethod" type="select" label="Method to use for profile generation (profmethod)" >
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	89 <option value="bin" selected="true">bin</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	90 <option value="binlin">binlin</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	91 <option value="binlinbase">binlinbase</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	92 <option value="intlin">intlin</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	93 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	94 -->
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	95 <conditional name="methods">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	96 <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	97 <option value="centWave" >centWave</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	98 <option value="matchedFilter" selected="true">matchedFilter</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	99 <option value="MSW">MSW</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	100 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	101
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	102 <!-- centWave Filter options -->
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	103 <when value="centWave">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	104 <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	105 <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	106
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	107 <conditional name="options_c">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	108 <param name="option" type="select" label="Advanced options" >
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	109 <option value="show">show</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	110 <option value="hide" selected="true">hide</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	111 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	112 <when value="show">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	113 <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	114 <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	115 <param name="integrate" type="select" label="peak limits method" help="[integrate]" >
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	116 <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	117 <option value="2">peak limits based on real data (more sensitive to noise)</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	118 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	119 <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	120 <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	121 </when>
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	122 <when value="hide">
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	123 </when>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	124 </conditional>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	125 </when>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	126
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	127 <!-- matched Filter options -->
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	128 <when value="matchedFilter">
26 626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 25 diff changeset	129 <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	130 <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	131 <conditional name="options_m">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	132 <param name="option" type="select" label="Advanced options" >
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	133 <option value="show">show</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	134 <option value="hide" selected="true">hide</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	135 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	136 <when value="show">
26 626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 25 diff changeset	137 <!--<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	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" />
26 626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 25 diff changeset	141 <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	142 </when>
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	143 <when value="hide">
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	144 </when>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	145 </conditional>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	146 </when>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	147
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	148 <!-- MSW Filter options -->
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	149 <when value="MSW">
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	150 <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	151 <option value="TRUE">TRUE</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	152 <option value="FALSE">FALSE</option>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	153 </param>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	154 <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	155 <param name="snthr" type="integer" value="3" label="SNR (Signal to Noise Ratio) threshold" help="[snthr]" />
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	156 <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	157 <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	158 <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	159 </when>
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	160 </conditional>
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	161
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	162
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	163 <expand macro="input_tic_bpc_pdf"/>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	164 </inputs>
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	165
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	166 <outputs>
25 dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	167 <data name="xsetRData" format="rdata.xcms.raw" label="${input.name.rsplit('.',1)[0]}.xset.RData" />
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	168 <data name="log" format="txt" label="${input.name.rsplit('.',1)[0]}.xset.log.txt" />
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	169
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	170 <!-- SINGLE MODE -->
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	171 <data name="ticsRawTab" format="tabular" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.tabular">
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	172 <filter>input.extension in ["mzxml","mzml","mzdata","netcdf"]</filter>
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	173 </data>
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	174 <data name="bpcsRawTab" format="tabular" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.tabular">
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	175 <filter>input.extension in ["mzxml","mzml","mzdata","netcdf"]</filter>
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	176 </data>
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	177
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	178 <!-- ZIP MODE -->
25 dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	179 <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv">
dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	180 <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	181 </data>
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	182 <data name="ticsRawPdf" format="pdf" from_work_dir="TICs.pdf" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.pdf">
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	183 <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	184 <filter>tic_bpc_pdf</filter>
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	185 </data>
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	186 <data name="bpcsRawPdf" format="pdf" from_work_dir="BPCs.pdf" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.pdf">
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	187 <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	188 <filter>tic_bpc_pdf</filter>
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	189 </data>
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	190 <collection name="ticsRawTabCollection" type="list" label="TIC raw tabular">
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	191 <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	192 <discover_datasets pattern="(?P<designation>.+)-TIC_mqc\.out" ext="tabular" visible="true" />
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	193 </collection>
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	194 <collection name="bpcsRawTabCollection" type="list" label="BPC raw tabular">
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	195 <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	196 <discover_datasets pattern="(?P<designation>.+)-BPC_mqc\.out" ext="tabular" visible="true" />
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	197 </collection>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	198 </outputs>
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	199
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	200 <tests>
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	201 <!--
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	202 <test>
25 dc4d3e2b9968 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312 lecorguille parents: 24 diff changeset	203 <param name="input" value="sacuri_current_root.zip" ftype="zip" />
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	204 <param name="methods\|method" value="centWave" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	205 <param name="methods\|ppm" value="25" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	206 <param name="methods\|peakwidth" value="20,50" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	207 <output name="log">
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	208 <assert_contents>
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	209 <has_text text="object with 4 samples" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	210 <has_text text="Time range: 3.5-1139.2 seconds (0.1-19 minutes)" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	211 <has_text text="Mass range: 57.9756-593.4086 m/z" />
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	212 <has_text text="Peaks: 1535 (about 384 per sample)" />
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	213 <has_text text="Peak Groups: 0" />
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	214 <has_text text="Sample classes: bio, blank" />
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	215 </assert_contents>
2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	216 </output>
10 00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	217 </test>-->
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	218 <test>
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	219 <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	220 <param name="methods\|method" value="centWave" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	221 <param name="methods\|ppm" value="25" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	222 <param name="methods\|peakwidth" value="20,50" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	223 <output name="log">
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	224 <assert_contents>
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	225 <has_text text="object with 4 samples" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	226 <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	227 <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	228 <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	229 <has_text text="Peak Groups: 0" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	230 <has_text text="Sample classes: KO, WT" />
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	231 </assert_contents>
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29 lecorguille parents: 6 diff changeset	232 </output>
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	233 <output_collection name="ticsRawTabCollection" type="list">
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	234 <element name="ko15" value="ko15-TIC_mqc.out" />
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	235 <element name="ko16" value="ko16-TIC_mqc.out" />
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	236 <element name="wt15" value="wt15-TIC_mqc.out" />
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	237 <element name="wt16" value="wt16-TIC_mqc.out" />
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	238 </output_collection>
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	239 <output_collection name="bpcsRawTabCollection" type="list">
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	240 <element name="ko15" value="ko15-BPC_mqc.out" />
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	241 <element name="ko16" value="ko16-BPC_mqc.out" />
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	242 <element name="wt15" value="wt15-BPC_mqc.out" />
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	243 <element name="wt16" value="wt16-BPC_mqc.out" />
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	244 </output_collection>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	245 </test>
20 d7971ea3ad1d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 717c02f887ce343ca55f862c8020aaf49f5581d8 lecorguille parents: 17 diff changeset	246 <!-- Passed but disable to save time for Travis" -->
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	247 <!--
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	248 <test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	249 <param name="inputs\|input" value="single_file" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	250 <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	251 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	252 <param name="methods\|ppm" value="25" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	253 <param name="methods\|peakwidth" value="20,50" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	254 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	255 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	256 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	257 <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	258 <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	259 <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	260 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	261 <has_text text="Sample classes: ." />
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 </output>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	264 </test>-->
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	265 <test>
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	266 <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	267 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	268 <param name="methods\|ppm" value="25" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	269 <param name="methods\|peakwidth" value="20,50" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	270 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	271 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	272 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	273 <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	274 <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	275 <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	276 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	277 <has_text text="Sample classes: ." />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	278 </assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	279 </output>
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	280 <output name="ticsRawTab" value="HU_neg_017-TIC_mqc.out" />
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	281 <output name="bpcsRawTab" value="HU_neg_017-BPC_mqc.out" />
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	282 </test>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	283 <test>
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	284 <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	285 <param name="methods\|method" value="centWave" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	286 <param name="methods\|ppm" value="56" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	287 <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	288 <output name="log">
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	289 <assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	290 <has_text text="object with 1 samples" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	291 <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	292 <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	293 <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	294 <has_text text="Peak Groups: 0" />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	295 <has_text text="Sample classes: ." />
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	296 </assert_contents>
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	297 </output>
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	298 <output name="ticsRawTab" value="MM14-TIC_mqc.out" />
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	299 <output name="bpcsRawTab" value="MM14-BPC_mqc.out" />
17 602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	300 </test>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	301 </tests>
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	302
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	303 <help><![CDATA[
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	304
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	305 @HELP_AUTHORS@
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	306
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	307 ============
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	308 Xcms.xcmsSet
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	309 ============
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	310
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	311 Description
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	312 -----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	313
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	314 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	315 You can read a tutorial on how to perform xcms preprocessing which is available here_.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	316
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	317 .. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	318
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	319
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	320 Workflow position
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	321 -----------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	322
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	323 Upstream tools
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	324
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	325 +------------------------+--------------------+-----------------------------+-----------+
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	326 \| Name \| output file \| format \| parameter \|
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	327 +------------------------+--------------------+-----------------------------+-----------+
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	328 \| Upload File \| Dataset Collection \| mzXML, mzML, mzData, netCDF \| NA \|
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	329 +------------------------+--------------------+-----------------------------+-----------+
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	330
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	331 Downstream tools
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	332
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	333 +---------------------------+--------------------+-----------------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	334 \| Name \| Output file \| Format \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	335 +===========================+====================+=================+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	336 \|xcms.group \| xset.RData \| rdata.xcms.raw \|
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	337 +---------------------------+--------------------+-----------------+
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	338
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	339
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	340 Example of a metabolomic workflow
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	341
28 b90e4f92e8b5 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 392e432529877680e80a7b338e20d69a42e53767 lecorguille parents: 26 diff changeset	342 .. image:: xcms_xcmsset_workflow.png
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	343
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 Input files
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	348 -----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	349
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	350 Choose your inputs
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	351 ------------------
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	352
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	353 +---------------------------+----------------------------------+
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	354 \| Parameter \| Format \|
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	355 +===========================+==================================+
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	356 \| OR : Single file \| mzXML, mzML, mzData, netCDF \|
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	357 +---------------------------+----------------------------------+
24 d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	358 \| OR : Zip file \| zip \|
d8915395681f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d lecorguille parents: 23 diff changeset	359 +---------------------------+----------------------------------+
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	360
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	361 You have two methods for your inputs:
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	362
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	363 * 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"
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	364
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	365 * Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	366
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	367 Single file
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	368 -----------
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	369
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	370 This method is recommended because:
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	371
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	372 * Since files are uploaded indivudially, they are smaller. And so they should be able to be uploaded using the Get Data tools.
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	373
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	374 * It allow you to launch your xcmsSet in parallele.
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	375
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	376 You just have to create a Dataset Collection as explain in this video_
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	377
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	378 .. _video: http://download.workflow4metabolomics.org/docs/170510_galaxy_xcms_dataset_collection.m4v
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	379
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	380
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	381 Zip file
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	382 --------
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	383
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	384 This method isn't recommended because zip file aren't really well integrated
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	385
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	386 Steps for creating the zip file
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	387
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	388 Step1: Creating your directory and hierarchize the subdirectories
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	389
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	390
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	391 \| 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).
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	392 \| Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	393 \| - arabidopsis/wild/01.raw
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	394 \| - arabidopsis/mutant/01.raw
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	395
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	396 Step2: Creating a zip file
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	397
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	398 \| Create your zip file (e.g.: arabidopsis.zip).
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	399
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	400 Step 3 : Uploading it to our Galaxy server
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	401
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	402 \| If your zip file is less than 2Gb, you get use the Get Data tool to upload it.
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	403 \| 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).
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	404 \| For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	405 \| Advices for converting your files for the XCMS input
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	406
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	407 Raw file format
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	408 ---------------
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	409
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	410 We recommend you to convert your raw files to mzXML in centroid mode (smaller files) and the files will be compatible with the xcms centWave method.
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	411
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	412 We recommend you the following parameters:
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	413
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	414 \| Use Filtering: True
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	415 \| Use Peak Picking: True
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	416 \| Peak Peaking: -Apply to MS Levels: All Levels (1-) : Centroid Mode
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	417 \| Use zlib: 64
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	418 \| Binary Encoding: 64
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	419 \| m/z Encoding: 64
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	420 \| Intensity Encoding: 64
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	421
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	422
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	423 ----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	424 Parameters
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	425 ----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	426
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	427 Extraction method for peaks detection
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	428 -------------------------------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	429
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	430 Matched Filter
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	431
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	432 \| 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	433 \| 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	434
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	435
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	436 cent Wave
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	437
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	438 \| This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	439 \| Due to the fact that peak centroids are used, a binning step is not necessary.
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	440 \| 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	441
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	442 MSW
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	443
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	444 \| 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	445 \| If you wish to have more details about the other parameters, you can read the following documents:
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	446 \| -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	447 \| -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	448
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	449
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	450 ------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	451 Output files
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	452 ------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	453
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	454 xset.RData: rdata.xcms.raw format
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	455
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	456 \| 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	457
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	458 @HELP_BCP_TIC@
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	459
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	460 sampleMetadata.tsv [if using zip]
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	461
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	462 \| Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed).
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	463 \| This file is necessary in the Batch correction and statictics steps of the workflow.
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	464
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	465 ---------------------------------------------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	466
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	467 ---------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	468 Working example
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	469 ---------------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	470
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	471 Input files
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	472 -----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	473
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	474 \| Dataset Collection -> build using this dataset_
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	475
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	476 .. _dataset: http://download.workflow4metabolomics.org/datasets/sacurine-neg-subset_mzXML.zip
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	477
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	478 Parameters
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	479 ----------
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	480
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	481 \| Method: centWave
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	482 \| Max tolerated ppm m/z deviation in consecutive scans in ppm: 25
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	483 \| Min,Max peak width in seconds: 10,40
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	484 \| Advanced option: show
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	485 \| Signal/Noise threshold: 50
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	486 \| Minimum difference in m/z for peaks with overlapping retention times: 1
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	487 \| Prefilter step for the first phase: 3,100
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	488
1bad16e5e4ae planemo upload lecorguille parents: diff changeset	489
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	490 ---------------------------------------------------
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	491
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	492 Changelog/News
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	493 --------------
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	494
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	495 Version 2.2.0 - 19/10/2017
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	496
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	497 - NEW: The TIC and BPC is new exported as tabular files to be visualized using MultiQC.
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	498
26 626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 25 diff changeset	499 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	500
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907 lecorguille parents: 16 diff changeset	501 - 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	502
26 626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf lecorguille parents: 25 diff changeset	503 - 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	504
16 f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	505 Version 2.0.11 - 22/12/2016
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	506
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	507 - BUGFIX: propose scanrange for all methods
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093 lecorguille parents: 15 diff changeset	508
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	509 Version 2.0.10 - 22/12/2016
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	510
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	511 - 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	512
13 68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 10 diff changeset	513 Version 2.0.9 - 06/07/2016
68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4 lecorguille parents: 10 diff changeset	514
15 1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94 lecorguille parents: 13 diff changeset	515 - 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	516
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	517 Version 2.0.8 - 06/04/2016
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	518
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	519 - TEST: refactoring to pass planemo test using conda dependencies
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	520
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	521
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	522 Version 2.0.7 - 10/02/2016
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	523
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	524 - BUGFIX: better management of errors. Datasets remained green although the process failed
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	525
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	526 - 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	527
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	528 - 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	529
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	530 - UPDATE: refactoring of internal management of inputs/outputs
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	531
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	532 - TEST: refactoring to feed the new report tool
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	533
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	534
29 5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9 lecorguille parents: 28 diff changeset	535 Version 2.0.2 - 18/01/2016
4 4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	536
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	537 - 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	538
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	539
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	540 Version 2.0.2 - 09/10/2015
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	541
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	542 - 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	543
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	544
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	545 Version 2.0.2 - 02/06/2015
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	546
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	547 - 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	548
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	549 - 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	550
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	551 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
4509e9dd03e4 planemo upload lecorguille parents: 3 diff changeset	552
1 2f5b78be1dd6 Uploaded lecorguille parents: 0 diff changeset	553 ]]></help>
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	554
6 60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e lecorguille parents: 5 diff changeset	555 <expand macro="citation" />
0 1bad16e5e4ae planemo upload lecorguille parents: diff changeset	556 </tool>

Mercurial > repos > lecorguille > xcms_xcmsset

annotate abims_xcms_xcmsSet.xml @ 29:5dba1c94fb94 draft