ipo: ipo4xcmsSet.xml annotate

annotate ipo4xcmsSet.xml @ 10:57f180a8eaae draft default tip

planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11

author	workflow4metabolomics
date	Mon, 11 Sep 2023 22:36:51 +0000
parents	364756ea5f42
children

rev	line source
10 57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11 workflow4metabolomics parents: 9 diff changeset	1 <tool id="ipo4xcmsSet" name="IPO for xcmsSet" version="@TOOL_VERSION@+galaxy1">
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	2
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	3 <description>IPO optimization process for xcms.findChromPeaks</description>
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	4
3 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
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	11 <command detect_errors="exit_code"><![CDATA[
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	12 LANG=C Rscript '$__tool_directory__/ipo4xcmsSet.r'
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	13
10 57f180a8eaae planemo upload for repository https://github.com/rietho/IPO commit d25c744220e416cce158161fa7dc3b0f153a5c11 workflow4metabolomics parents: 9 diff changeset	14 singlefile_galaxyPath '$input' singlefile_sampleName '$input.element_identifier'
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	15
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	16 samplebyclass $samplebyclass
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	17
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	18 ## profmethod $profmethod
6 03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce lecorguille parents: 5 diff changeset	19 @COMMAND_NSLAVES@
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	20 method $methods.method
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	21 #if $methods.method == "centWave":
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	22 ppm "c($methods.section_centwave_optiomizable.ppm)"
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	23 min_peakwidth "c($methods.section_centwave_optiomizable.min_peakwidth)"
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	24 max_peakwidth "c($methods.section_centwave_optiomizable.max_peakwidth)"
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	25 mzdiff "c($methods.section_centwave_optiomizable.mzdiff)"
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	26
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	27 snthresh $methods.section_centwave_non_optiomizable.snthresh
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	28 integrate $methods.section_centwave_non_optiomizable.integrate
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	29 noise $methods.section_centwave_non_optiomizable.noise
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	30 prefilter "c($methods.section_centwave_non_optiomizable.prefilter)"
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	31
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	32 #elif $methods.method == "matchedFilter":
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	33 fwhm "c($methods.section_matchedfilter_optiomizable.fwhm)"
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	34 mzdiff "c($methods.section_matchedfilter_optiomizable.mzdiff)"
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	35
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	36 step $methods.section_matchedfilter_non_optimizable.step
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	37 steps $methods.section_matchedfilter_non_optimizable.steps
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	38 max $methods.section_matchedfilter_non_optimizable.max
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	39 snthresh $methods.section_matchedfilter_non_optimizable.snthresh
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	40 #end if
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	41 ]]></command>
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	42
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	43 <inputs>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	44
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	45 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. See the help section below." />
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	46
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	47 <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	48
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	49 <conditional name="methods">
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	50 <param argument="method" type="select" label="Extraction method for peaks detection (findChromPeaks)" help="See the help section below">
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	51 <option value="centWave" >centWave</option>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	52 <option value="matchedFilter" selected="true">matchedFilter</option>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	53 </param>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	54
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	55 <!-- centWave Filter options -->
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	56 <when value="centWave">
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	57 <section name="section_centwave_optiomizable" title="Optimizable parameters" expanded="True">
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	58 <param argument="ppm" type="text" value="17,32" label="Range or a fixed value for Max tolerated ppm m/z deviation in consecutive scans in ppm" optional="false" help="(ex: 25 or 17,32)">
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	59 <expand macro="input_validator_range_integer"/>
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	60 </param>
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	61 <param argument="min_peakwidth" type="text" value="12,18" label="Range or a fixed value for Min peak width range in seconds" optional="true" help="(ex: 12,18)">
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	62 <expand macro="input_validator_range_float"/>
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	63 </param>
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	64 <param argument="max_peakwidth" type="text" value="35,65" label="Range or a fixed value for Max peak width range in seconds" optional="true" help="(ex: 35,65)">
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	65 <expand macro="input_validator_range_float"/>
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	66 </param>
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	67 <param argument="mzdiff" type="text" value="-0.001,0.010" label="Range or a fixed value for Minimum difference in m/z for peaks with overlapping retention times" help="Can be negative to allow overlap (ex: -0.001,0.010)">
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	68 <expand macro="input_validator_range_float_neg"/>
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	69 </param>
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	70 </section>
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	71
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	72 <section name="section_centwave_non_optiomizable" title="Non optimizable parameters" expanded="True">
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	73 <param argument="snthresh" type="integer" value="10" label="Signal/Noise threshold" help="Signal to noise ratio cutoff" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	74 <param argument="integrate" type="select" label="Peak limits method" >
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	75 <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option>
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	76 <option value="2">peak limits based on real data (more sensitive to noise)</option>
4 9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	77 </param>
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	78 <param argument="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/>
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	79 <param argument="noise" type="integer" value="0" label="Noise filter" help="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"/>
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	80 </section>
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	81 </when>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	82
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	83 <!-- matched Filter options -->
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	84 <when value="matchedFilter">
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	85 <section name="section_matchedfilter_optiomizable" title="Optimizable parameters" expanded="True">
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	86 <param argument="fwhm" type="text" value="25,35" label="Range or a fixed value for Full width at half maximum of matched filtration gaussian model peak" optional="true" help="Only used to calculate the actual sigma (ex: 25,35)">
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	87 <expand macro="input_validator_range_integer"/>
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	88 </param>
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	89 <param argument="mzdiff" type="text" value="0.4,0.7" label="Range or a fixed value for Minimum difference in m/z for peaks with overlapping Retention Times" help="By default: 0.8-step*steps (ex: 0.4,0.7)">
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	90 <expand macro="input_validator_range_float_neg"/>
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	91 </param>
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	92 </section>
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	93
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	94 <section name="section_matchedfilter_non_optimizable" title="Non optimizable parameters" expanded="True">
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	95 <param argument="step" type="float" value="0.1" label="Step size to use for profile generation" help="The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	96 <param argument="steps" type="integer" value="2" label="Number of steps to merge prior to filtration" help="The peak identification algorithm combines a given number of EIBPCs prior to filtration and peak detection, as defined by the steps argument" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	97 <param argument="max" type="integer" value="5" label="Maximum number of peaks per extracted ion chromatogram" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	98 <param argument="snthresh" type="integer" value="10" label="Signal to noise ratio cutoff" />
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	99 </section>
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	100 </when>
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	101 </conditional>
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	102
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	103
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	104 </inputs>
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	105
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	106 <outputs>
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	107 <data name="xsetRData" format="rdata.xcms.raw" label="ipo4xcmsSet.RData" from_work_dir="ipo4xcmsSet.RData" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	108 <data name="parametersOutput" format="tabular" label="IPO_parameters4xcmsSet.tsv" from_work_dir="IPO_parameters4xcmsSet.tsv" />
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	109 </outputs>
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	110
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	111 <tests>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	112 <test>
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	113 <param name="input" value="MM14.mzML" ftype="mzxml" />
4 9fa5856f6184 planemo upload commit 98cb24e57c0ce8ac3294e8c7e87aee337ac29f62 lecorguille parents: 3 diff changeset	114 <param name="samplebyclass" value="0" />
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	115 <conditional name="methods">
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	116 <param name="method" value="centWave" />
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	117 <section name="section_centwave_optiomizable" >
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	118 <param name="min_peakwidth" value="3,9.5" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	119 <param name="max_peakwidth" value="10,20" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	120 <param name="ppm" value="56" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	121 <param name="mzdiff" value="-0.001" />
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	122 </section>
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	123 </conditional>
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	124 <output name="parametersOutput" file="MM14_IPO_parameters4xcmsSet_peakwidth.tsv" />
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	125 </test>
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	126 <test>
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	127 <param name="input" value="MM14.mzML" ftype="mzxml" />
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	128 <param name="samplebyclass" value="0" />
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	129 <conditional name="methods">
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	130 <param name="method" value="centWave" />
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	131 <section name="section_centwave_optiomizable" >
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	132 <param name="ppm" value="50,60" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	133 <param name="min_peakwidth" value="3.325" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	134 <param name="max_peakwidth" value="11.0" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	135 <param name="mzdiff" value="-0.001" />
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	136 </section>
dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	137 </conditional>
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	138 <output name="parametersOutput">
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	139 <assert_contents>
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	140 <!-- is XML escape code for tab -->
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	141 <has_line line="ppm 60" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	142 <has_line line="min_peakwidth 3.325" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	143 <has_line line="max_peakwidth 11" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	144 <has_line line="mzdiff -0.001" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	145 <has_line line="prefilter 3" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	146 <has_line line="snthresh 10" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	147 <has_line line="integrate 1" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	148 <has_line line="noise 0" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	149 <has_line line="value_of_prefilter 100" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	150 <has_line line="mzCenterFun wMean" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	151 <has_line line="fitgauss FALSE" />
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	152 </assert_contents>
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	153 </output>
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	154 </test>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	155 </tests>
7 dd0a593dded1 planemo upload commit c3ffcc9ea76a0e143e11613e6841ee59a28578fd lecorguille parents: 6 diff changeset	156
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	157 <help><![CDATA[
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	158
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	159 @HELP_AUTHORS@
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	160
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	161 ===============
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	162 IPO.ipo4xcmsSet
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	163 ===============
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	164
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	165 -----------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	166 Description
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	167 -----------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	168
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	169 A Tool for automated Optimization of XCMS Parameters
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	170
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	171
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	172 -----------------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	173 Workflow position
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	174 -----------------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	175
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	176 Upstream tools
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	177
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	178 ========================= ========================
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	179 Name Format
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	180 ========================= ========================
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	181 Upload File mzxml,mzml,mzdata,netcdf
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	182 ========================= ========================
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	183
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	184 The easier way to process is to create a Dataset Collection of the type List
3 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 Downstream tools
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 \| Name \| Output file \| Format \|
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	191 +===========================+======================+=================+
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	192 \|xcms.xcmsSet \| parametersOutput.tsv \| Tabular \|
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	193 +---------------------------+--------------------+-------------------+
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	194
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 -----------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	198 Input files
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	199 -----------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	200
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	201 Advices for converting your files for the XCMS input
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	202 ----------------------------------------------------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	203
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	204 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	205
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	206 We recommend you the following parameters:
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	207
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	208 Use Filtering: True
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	209
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	210 Use Peak Picking: True
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	211
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	212 Peak Peaking -Apply to MS Levels: All Levels (1-) : Centroid Mode
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	213
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	214 Use zlib: 64
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	215
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	216 Binary Encoding: 64
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	217
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	218 m/z Encoding: 64
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	219
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	220 Intensity Encoding: 64
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	221
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	222
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	223 ----------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	224 Parameters
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	225 ----------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	226
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	227 Extraction method for findChromPeaks
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	228 -------------------------------------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	229
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	230 MatchedFilter
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	231
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	232 \| The matchedFilter algorithm identifies peaks in the chromatographic time domain as described in [Smith 2006]. The intensity values are binned by cutting The LC/MS data into slices (bins) of a mass unit (‘binSize’ m/z) wide. Within each bin the maximal intensity is selected. The chromatographic peak detection is then performed in each bin by extending it based on the ‘steps’ parameter to generate slices comprising bins ‘current_bin - steps +1’ to ‘current_bin + steps - 1’. Each of these slices is then filtered with matched filtration using a second-derative Gaussian as the model peak shape. After filtration peaks are detected using a signal-to-ratio cut-off. For more details and illustrations see [Smith 2006].
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	233 \| See the MatchedFilter_manual_
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	234
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	235 CentWave
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	236
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	237 \| The centWave algorithm perform peak density and wavelet based chromatographic peak detection for high resolution LC/MS data in centroid mode [Tautenhahn 2008].
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	238 \| 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	239 \| 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.
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	240 \| See the CentWave_manual_
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	241
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	242 .. _MatchedFilter_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-matchedFilter.html#heading-2
364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	243 .. _CentWave_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-centWave.html#heading-2
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	244
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	245 ---------------------------------------------------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	246
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	247 Changelog/News
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	248 --------------
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	249
9 364756ea5f42 "planemo upload for repository https://github.com/rietho/IPO commit 5083f3b5800bdd8515519f2f6398046b41e1df97" workflow4metabolomics parents: 7 diff changeset	250 @HELP_NEWVERSION_1_10_0_0@
3 9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	251
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	252 ]]></help>
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	253
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	254 <expand macro="citation" />
9f1e18bc8ce3 planemo upload commit ceb25d29a013b58d3476323f202276e7c876648a-dirty lecorguille parents: diff changeset	255 </tool>

Mercurial > repos > lecorguille > ipo

annotate ipo4xcmsSet.xml @ 10:57f180a8eaae draft default tip