ipo: ipo4xcmsSet.xml annotate

annotate ipo4xcmsSet.xml @ 5:d63c80d54b24 draft

planemo upload commit ed7e37099389cdc575d4163ed277b882a0043e5a-dirty

author	lecorguille
date	Thu, 29 Sep 2016 16:55:16 -0400
parents	9fa5856f6184
children	03fdfbd914ab

rev	line source
4 9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	1 <tool id="ipo4xcmsSet" name="IPO for xcmsSet" version="0.0.3">
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	2
5 d63c80d54b24 planemo upload commit ed7e37099389cdc575d4163ed277b882a0043e5a-dirty lecorguille parents: 4 diff changeset	3 <description>IPO optimization process for xcms.xcmsSet</description>
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	4
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	5 <macros>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	6 <import>macros.xml</import>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	7 </macros>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	8
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	9 <expand macro="requirements"/>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	10 <expand macro="stdio"/>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	11
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	12 <command><![CDATA[
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	13 @COMMAND_SCRIPT@
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	14
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	15 #if $inputs.input == "zip_file":
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	16 zipfile $inputs.zip_file
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	17 #elif $inputs.input == "single_file":
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	18 singlefile_galaxyPath $inputs.single_file singlefile_sampleName $inputs.single_file.name
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	19 #end if
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	20
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	21 parametersOutput $parametersOutput
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	22
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	23 samplebyclass $samplebyclass
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	24
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	25 ## profmethod $profmethod
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	26 nSlaves \${GALAXY_SLOTS:-1} method $methods.method
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	27 #if $methods.method == "centWave":
4 9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	28 ppm "c($methods.ppm)"
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	29 min_peakwidth "c($methods.min_peakwidth)"
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	30 max_peakwidth "c($methods.max_peakwidth)"
4 9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	31 #if $methods.options_c.option == "show":
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	32 mzdiff "c($methods.options_c.mzdiff)"
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	33 snthresh "c($methods.options_c.snthresh)"
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	34 integrate "c($methods.options_c.integrate)"
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	35 noise "c($methods.options_c.noise)"
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	36 prefilter "c($methods.options_c.prefilter)"
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	37 prefilter_value "c($methods.options_c.prefilter_value)"
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	38 #end if
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	39 #elif $methods.method == "matchedFilter":
4 9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	40 step "c($methods.step)"
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	41 fwhm "c($methods.fwhm)"
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	42 #if $methods.options_m.option == "show":
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	43 sigma "c($methods.options_m.sigma)"
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	44 max "c($methods.options_m.max)"
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	45 snthresh "c($methods.options_m.snthresh)"
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	46 mzdiff "c($methods.options_m.mzdiff)"
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	47 steps "c($methods.options_m.steps)"
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	48 #end if
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	49 #end if
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	50
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	51 @COMMAND_LOG_EXIT@ 2> /tmp/log.err
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	52 ]]></command>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	53
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	54 <inputs>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	55
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	56 <conditional name="inputs">
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	57 <param name="input" type="select" label="Choose your inputs method" >
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	58 <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	59 <option value="single_file">mzXML file from your history</option>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	60 </param>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	61 <when value="zip_file">
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	62 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	63 </when>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	64 <when value="single_file">
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	65 <param name="single_file" type="data" format="mzxml" label="Single file" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	66 </when>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	67 </conditional>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	68
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	69 <param name="samplebyclass" type="integer" value="2" label="Number of samples used per class to estimate the best parameters" help="Set to 0 to use the whole dataset. To save time, reduce this number" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	70
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	71 <conditional name="methods">
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	72 <param name="method" type="select" label="Extraction method for peaks detection" help="[method] See the help section below">
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	73 <option value="centWave" >centWave</option>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	74 <option value="matchedFilter" selected="true">matchedFilter</option>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	75 </param>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	76
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	77 <!-- centWave Filter options -->
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	78 <when value="centWave">
4 9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	79 <param name="ppm" type="text" value="17,32" label="Range for Max tolerated ppm m/z deviation in consecutive scans in ppm" optional="false" help="[ppm] (ex: 25 or 17,32)" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	80 <param name="min_peakwidth" type="text" value="15,25" label="Range for Min peak width range in seconds" optional="true" help="[min_peakwidth] (ex: 20 or 12,18)" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	81 <param name="max_peakwidth" type="text" value="45,55" label="Range for Max peak width range in seconds" optional="true" help="[max_peakwidth] (ex: 50 or 35,65)" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	82 <conditional name="options_c">
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	83 <param name="option" type="select" label="Advanced options" >
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	84 <option value="show">show</option>
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	85 <option value="hide" selected="true">hide</option>
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	86 </param>
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	87 <when value="show">
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	88 <param name="snthresh" type="text" value="10" label="Range for Signal/Noise threshold" help="[snthresh] Signal to noise ratio cutoff (ex: 10 or 5,15)" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	89 <param name="mzdiff" type="text" value="-0.001" label="Range for Min m/z difference" help="[mzdiff] Min m/z difference for peaks with overlapping RT (ex: -0.001 or -0.001,0.010)" />
5 d63c80d54b24 planemo upload commit ed7e37099389cdc575d4163ed277b882a0043e5a-dirty lecorguille parents: 4 diff changeset	90 <param name="integrate" type="select" label="Peak limits method" help="[integrate]" >
4 9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	91 <option value="1">1 - peak limits based on smoothed 2nd derivative (less precise)</option>
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	92 <option value="2">2 - peak limits based on real data (more sensitive to noise)</option>
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	93 </param>
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	94 <param name="prefilter" type="text" value="3" label="Range for the k value for the Prefilter step for the first phase" help="[prefilter] Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’ (ex: 3 or 2,3)"/>
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	95 <param name="prefilter_value" type="text" value="100" label="Range for the I value for the Prefilter step for the first phase" help="[prefilter_value] Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’ (ex: 100 or 95,105)"/>
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	96 <param name="noise" type="text" value="0" label="Range for the 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 (ex: 0 or 0,0.1)"/>
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	97 </when>
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	98 <when value="hide" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	99 </conditional>
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	100 </when>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	101
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	102 <!-- matched Filter options -->
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	103 <when value="matchedFilter">
4 9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	104 <param name="step" type="text" value="0.1" label="Range for Step size to use for profile generation" optional="true" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size (ex: 0 or 0.05,0.15)" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	105 <param name="fwhm" type="text" value="25,35" label="Range for Full width at half maximum of matched filtration gaussian model peak" optional="true" help="[fwhm] Only used to calculate the actual sigma (ex: 30 or 25,35)" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	106 <conditional name="options_m">
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	107 <param name="option" type="select" label="Advanced options" >
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	108 <option value="show">show</option>
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	109 <option value="hide" selected="true">hide</option>
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	110 </param>
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	111 <when value="show">
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	112 <param name="sigma" type="text" value="0" label="sigma" help="Range for standard deviation (fwhm/2.3548) (ex: 0 or 0,1)" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	113 <param name="max" type="text" value="5" label="Range for Maximum number of peaks per extracted ion chromatogram" help="[max] (ex: 5 or 4,6)" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	114 <param name="snthresh" type="text" value="10" label="Range for Signal to noise ratio cutoff" help="[snthresh] (ex: 10 or 3,17)" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	115 <param name="steps" type="text" value="2" label="Range for 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 (ex: 2 or 1,3)" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	116 <param name="mzdiff" type="text" value="0" label="m/z difference" help="Range for min m/z difference for peaks with overlapping RT (0.8-step*steps) (ex: 2 or 1,3)" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	117 </when>
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	118 <when value="hide" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	119 </conditional>
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	120 </when>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	121 </conditional>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	122
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	123
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	124 </inputs>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	125
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	126 <outputs>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	127 <data name="parametersOutput" format="tabular" label="IPO_parameters4xcmsSet.tsv" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	128 <data name="log" format="txt" label="ipo4xcmsSet.log.txt" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	129 </outputs>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	130
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	131 <tests>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	132 <test>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	133 <param name="inputs\|input" value="single_file" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	134 <param name="inputs\|single_file" value="MM14.mzML" ftype="mzxml" />
4 9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	135 <param name="samplebyclass" value="0" />
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	136 <param name="methods\|method" value="centWave" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	137 <param name="methods\|ppm" value="56" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	138 <param name="methods\|min_peakwidth" value="3,9.5" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	139 <param name="methods\|max_peakwidth" value="10,20" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	140 <output name="parametersOutput" file="MM14_IPO_parameters4xcmsSet.tsv" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	141 </test>
4 9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	142 <!-- Too long for Travis CI -->
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	143 <!--<test>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	144 <param name="inputs\|input" value="zip_file" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	145 <param name="inputs\|zip_file" value="sacuri_2files.zip" ftype="zip" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	146 <param name="samplebyclass" value="1" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	147 <param name="methods\|method" value="centWave" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	148 <param name="methods\|ppm" value="25" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	149 <param name="methods\|min_peakwidth" value="20,30" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	150 <param name="methods\|max_peakwidth" value="45,55" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	151 <output name="parametersOutput" file="sacuri_2files_centWave_IPO_parameters4xcmsSet.tsv" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	152 </test>-->
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	153 <!-- Too long for Travis CI -->
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	154 <!--<test>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	155 <param name="inputs\|input" value="zip_file" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	156 <param name="inputs\|zip_file" value="sacuri_2files.zip" ftype="zip" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	157 <param name="samplebyclass" value="1" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	158 <param name="methods\|method" value="matchedFilter" />
4 9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	159 <param name="methods\|step" value="0.05,0.15" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	160 <param name="methods\|fwhm" value="25,35" />
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	161 <output name="parametersOutput" file="sacuri_2files_matchedFilter_IPO_parameters4xcmsSet.tsv" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	162 </test>-->
4 9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	163 <!--Failed:
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	164 Error in resultIncreased(history) :
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	165 No isotopes have been detected, peak picking not optimizable by IPO!-->
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	166 <!--<test>
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	167 <param name="inputs\|input" value="zip_file" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	168 <param name="inputs\|zip_file" value="faahKO_reduce.zip" ftype="zip" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	169 <param name="methods\|method" value="centWave" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	170 <param name="methods\|ppm" value="25" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	171 <param name="methods\|min_peakwidth" value="15,25" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	172 <param name="methods\|min_peakwidth" value="20,30" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	173 <param name="methods\|max_peakwidth" value="45,55" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	174 <output name="parametersOutput" file="faahKO_IPO_parameters4xcmsSet.tsv" />
9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	175 </test>-->
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	176 </tests>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	177
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	178 <help><![CDATA[
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	179
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	180 @HELP_AUTHORS@
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	181
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	182 ===============
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	183 IPO.ipo4xcmsSet
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	184 ===============
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	185
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	186 -----------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	187 Description
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	188 -----------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	189
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	190 A Tool for automated Optimization of XCMS Parameters
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	191
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	192
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	193 -----------------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	194 Workflow position
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	195 -----------------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	196
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	197 Upstream tools
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	198
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	199 ========================= ================= ======= =========
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	200 Name output file format parameter
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	201 ========================= ================= ======= =========
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	202 NA NA zip NA
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	203 ========================= ================= ======= =========
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	204
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	205
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	206 Downstream tools
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	207
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	208 +---------------------------+----------------------+-----------------+
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	209 \| Name \| Output file \| Format \|
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	210 +===========================+======================+=================+
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	211 \|xcms.xcmsSet \| parametersOutput.tsv \| Tabular \|
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	212 +---------------------------+--------------------+-------------------+
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	213
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	214
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	215
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	216 -----------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	217 Input files
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	218 -----------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	219
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	220 +---------------------------+------------+
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	221 \| Parameter : num + label \| Format \|
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	222 +===========================+============+
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	223 \| 1 : Choose your inputs \| zip \|
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	224 +---------------------------+------------+
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	225
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	226 Choose your inputs
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	227
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	228 You have two methods for your inputs:
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	229
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	230 \| Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	231 \| library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories.
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	232
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	233 Steps for creating the zip file
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	234 -------------------------------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	235
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	236 Step1: Creating your directory and hierarchize the subdirectories
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	237
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	238
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	239 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).
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	240
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	241 Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	242 arabidopsis/wild/01.raw
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	243 arabidopsis/mutant/01.raw
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	244
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	245 Step2: Creating a zip file
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	246
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	247 Create your zip file (e.g.: arabidopsis.zip).
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	248
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	249 Step 3 : Uploading it to our Galaxy server
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	250
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	251 If your zip file is less than 2Gb, you get use the Get Data tool to upload it.
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	252
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	253 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).
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	254
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	255 For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	256
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	257 Advices for converting your files for the XCMS input
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	258 ----------------------------------------------------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	259
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	260 We recommend you to convert your raw files to mzXML in centroid mode (smaller files) and the files will be compatible with the xmcs centWave method.
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	261
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	262 We recommend you the following parameters:
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	263
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	264 Use Filtering: True
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	265
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	266 Use Peak Picking: True
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	267
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	268 Peak Peaking -Apply to MS Levels: All Levels (1-) : Centroid Mode
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	269
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	270 Use zlib: 64
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	271
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	272 Binary Encoding: 64
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	273
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	274 m/z Encoding: 64
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	275
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	276 Intensity Encoding: 64
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	277
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	278
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	279 ----------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	280 Parameters
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	281 ----------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	282
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	283 Extraction method for peaks detection
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	284 -------------------------------------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	285
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	286 Matched Filter
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	287
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	288 \| One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm.
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	289 \| For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002).
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	290
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	291
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	292 cent Wave
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	293
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	294 \| This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode.
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	295 \| Due to the fact that peak centroids are used, a binning step is not necessary.
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	296 \| 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.
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9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	298
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	299 ------------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	300 Output files
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	301 ------------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	302
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	303 IPO_parameters4xcmsSet.tsv
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	304
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	305 \| Optimal parameters for xcmsSet
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	306
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	307
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	308 ---------------------------------------------------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	309
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	310 Changelog/News
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	311 --------------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	312
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	313
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9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	315 ]]></help>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	316
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	317 <expand macro="citation" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	318 </tool>

Mercurial > repos > lecorguille > ipo

annotate ipo4xcmsSet.xml @ 5:d63c80d54b24 draft