camera_annotate: abims_CAMERA_annotateDiffreport.xml annotate

annotate abims_CAMERA_annotateDiffreport.xml @ 15:6139bfcc95cb draft

planemo upload commit 98f8d5d3e1a4356b411f16644ffa4da444ac2bdb

author	lecorguille
date	Thu, 01 Mar 2018 08:29:32 -0500
parents	225cb8347572
children	a2c49996603e

rev	line source
15 6139bfcc95cb planemo upload commit 98f8d5d3e1a4356b411f16644ffa4da444ac2bdb lecorguille parents: 14 diff changeset	1 <tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.2">
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	2
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	3 <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	4
9 7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	5 <macros>
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	6 <import>macros.xml</import>
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	7 </macros>
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	8
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	9 <expand macro="requirements"/>
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	10 <expand macro="stdio"/>
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	11
8 8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	12 <command><![CDATA[
9 7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	13 @COMMAND_CAMERA_SCRIPT@
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	14 xfunction annotatediff
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	15 image '$image'
8 8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	16
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	17 nSlaves \${GALAXY_SLOTS:-1}
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	18
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	19 ## output
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	20 variableMetadataOutput '$variableMetadata'
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	21 dataMatrixOutput '$datamatrix'
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	22
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	23 ## groupFWHM
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	24 sigma $groupfwhm.sigma
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	25 perfwhm $groupfwhm.perfwhm
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	26
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	27 ## findGeneral
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	28 ppm $findgeneral.ppm
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	29 mzabs $findgeneral.mzabs
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	30
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	31 ## findIsotopes
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	32 maxcharge $findisotopes.maxcharge
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	33 maxiso $findisotopes.maxiso
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	34 minfrac $findisotopes.minfrac
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	35
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	36 quick $quick_block.quick
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	37 #if $quick_block.quick == "FALSE":
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	38 xsetRdataOutput '$rdata_quick_false'
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	39
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	40 ## groupcorr
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	41 cor_eic_th $quick_block.groupcorr.cor_eic_th
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	42 graphMethod $quick_block.groupcorr.graphMethod
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	43 pval $quick_block.groupcorr.pval
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	44 calcCiS $quick_block.groupcorr.calcCiS
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	45 calcIso $quick_block.groupcorr.calcIso
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	46 calcCaS $quick_block.groupcorr.calcCaS
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	47
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	48 ## findadducts
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	49 polarity $quick_block.findadducts.polarity
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	50 max_peaks $quick_block.findadducts.max_peaks
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	51 #if $quick_block.findadducts.rules_block.rules_select == "FALSE":
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	52 multiplier $quick_block.findadducts.rules_block.multiplier
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	53 #else
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	54 rules $quick_block.findadducts.rules_block.rules
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	55 #end if
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	56 #else
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	57 xsetRdataOutput '$rdata_quick_true'
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	58 #end if
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	59
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	60 #if $diffreport.options.option == "show":
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	61 ## diffreport
8 8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	62 runDiffreport TRUE
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	63 eicmax $diffreport.options.eicmax
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	64 eicwidth $diffreport.options.eicwidth
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	65 value $diffreport.options.value
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	66 sortpval $diffreport.options.sortpval
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	67 h $diffreport.options.h
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	68 w $diffreport.options.w
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	69 mzdec $diffreport.options.mzdec
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	70 #end if
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	71
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	72 @COMMAND_PEAKLIST@
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	73
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	74 @COMMAND_FILE_LOAD@
9 7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	75
8 8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	76 ]]></command>
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	77
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	78 <inputs>
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	79
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	80
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	81 <param name="image" type="data" label="RData file" format="rdata.xcms.fillpeaks,rdata" help="output file from another function xcms (fillPeaks)" />
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	82
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	83 <section name="groupfwhm" title="Group co-eluted peaks based on RT [groupFWHM]" expanded="True">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	84 <param name="sigma" type="integer" value="6" label="Multiplier of the standard deviation" help="[sigma]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	85 <param name="perfwhm" type="float" value="0.6" max="1" min="0" label="Percentage of FWHM width" help="[perfwhm]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	86 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	87
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	88 <section name="findgeneral" title="Annotation general options" expanded="True">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	89 <param name="ppm" type="integer" value="5" label="General ppm error" help="[ppm]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	90 <param name="mzabs" type="float" value="0.015" label="General absolut error in m/z" help="[mzabs]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	91 </section>
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	92
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	93 <section name="findisotopes" title="Annotate Isotopes [findIsotopes]" expanded="True">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	94 <param name="maxcharge" type="integer" value="3" label="Max. ion charge" help="[maxcharge]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	95 <param name="maxiso" type="integer" value="4" label="Max. number of expected isotopes" help="[maxiso]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	96 <param name="minfrac" type="float" value="0.5" max="1" min="0" label="The percentage number of samples, which must satisfy the C12/C13 rule for isotope annotation" help="[minfrac]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	97 </section>
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	98
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	99 <conditional name="quick_block">
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	100 <param name="quick" type="select" label="Mode" help="[quick] If TRUE, use only groupFWHM and findIsotopes functions. Else if FALSE, use also groupCorr and findAdducts">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	101 <option value="FALSE" selected="true">All functions</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	102 <option value="TRUE">Only groupFWHM and findIsotopes functions [quick]</option>
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	103 </param>
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	104 <when value="FALSE">
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	105
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	106 <section name="groupcorr" title="Verifying grouping co-eluted peaks [groupCorr]" expanded="True">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	107 <param name="cor_eic_th" type="float" value="0.75" max="1" min="0" label="groupCorr: correlation threshold (0..1)" help="[cor_eic_th]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	108 <param name="graphMethod" type="select" label="groupCorr: Method selection for grouping peaks after correlation analysis into pseudospectra" help="[graphMethod]">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	109 <option value="hcs" selected="true">hcs</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	110 <option value="lpc">lpc</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	111 </param>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	112 <param name="pval" type="float" value="0.05" max="1" min="0" label="groupCorr: significant correlation threshold" help="[pval]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	113 <param name="calcCiS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation inside samples for peak grouping" help="[calcCiS]"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	114 <param name="calcIso" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use isotopic relationship for peak grouping" help="[calcIso]"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	115 <param name="calcCaS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation across samples for peak grouping" help="[calcCaS]"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	116 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	117
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	118 <section name="findadducts" title="Annotate Adducts [findAdducts]" expanded="True">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	119 <param name="polarity" type="select" label="Which polarity mode was used for measuring of the ms sample" help="polarity">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	120 <option value="positive" >positive</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	121 <option value="negative" selected="true">negative</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	122 </param>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	123 <param name="max_peaks" type="integer" value="100" label="How much peaks will be calculated in every thread using the parallel mode" help="[max_peaks]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	124 <conditional name="rules_block">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	125 <param name="rules_select" type="select" label="Use a personal ruleset file">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	126 <option value="TRUE">TRUE</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	127 <option value="FALSE" selected="true">FALSE</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	128 </param>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	129 <when value="FALSE">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	130 <param name="multiplier" type="integer" value="3" label="If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" help="[multiplier]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	131 </when>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	132 <when value="TRUE">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	133 <param name="rules" type="data" format="csv" label="User defined ruleset" help="[rules]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	134 </when>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	135 </conditional>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	136 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	137
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	138 </when>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	139 <when value="TRUE">
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	140 <param name="polarity" type="hidden" value="quick" label="for the output label" help="for the output label" />
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	141 </when>
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	142 </conditional>
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	143
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	144 <!-- Diffreport specific parameters -->
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	145 <section name="diffreport" title="Statistics and results export: [diffreport]" expanded="True">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	146 <conditional name="options">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	147 <param name="option" type="select" label="Number of condition">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	148 <option value="hide" selected="true">One condition</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	149 <option value="show">Two or more conditions</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	150 </param>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	151 <when value="show">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	152 <param name="eicmax" type="integer" value="0" label="Number of the most significantly different analytes to create EICs for" help="[eicmax]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	153 <param name="eicwidth" type="integer" value="200" label="Width (in seconds) of EICs produced" help="[eicwidth]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	154 <param name="value" type="select" label="Intensity values to be used for the diffreport" help="[value]">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	155 <option value="into" selected="true">into</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	156 <option value="maxo" >maxo</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	157 <option value="intb">intb</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	158 </param>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	159 <param name="h" type="integer" value="480" label="Numeric variable for the height of the eic and boxplots that are printed out" help="[height]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	160 <param name="w" type="integer" value="640" label="Numeric variable for the width of the eic and boxplots print out made" help="[width]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	161 <param name="mzdec" type="integer" value="2" label="Number of decimal places of title m/z values in the eic plot" help="[mzdec]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	162 <param name="sortpval" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="logical indicating whether the reports should be sorted by p-value" help="[sortpval]"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	163 </when>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	164 <when value="hide">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	165 </when>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	166 </conditional>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	167 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	168
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	169 <expand macro="input_peaklist"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	170 <expand macro="input_file_load"/>
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	171 </inputs>
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	172
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	173 <outputs>
3 729991209550 Uploaded mmonsoor parents: 0 diff changeset	174 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" />
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	175 <data name="datamatrix" format="tabular" label="${image.name[:-6]}.annotate.dataMatrix.tsv" />
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	176 <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata" >
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	177 <filter>quick_block['quick'] == 'FALSE'</filter>
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	178 <change_format>
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	179 <when input="quick_block.findadducts.polarity" value="positive" format="rdata.camera.positive" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	180 <when input="quick_block.findadducts.polarity" value="negative" format="rdata.camera.negative" />
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	181 </change_format>
3 729991209550 Uploaded mmonsoor parents: 0 diff changeset	182 </data>
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	183 <data name="rdata_quick_true" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.quick.Rdata" >
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	184 <filter>quick_block['quick'] == 'TRUE'</filter>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	185 </data>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	186 <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="true">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	187 <filter>diffreport['options']['option'] == 'show'</filter>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	188 <discover_datasets pattern="__designation_and_ext__" directory="pdf" visible="true" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	189 <discover_datasets pattern="__designation_and_ext__" directory="tabular" visible="true" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	190 </data>
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	191 </outputs>
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	192
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	193 <tests>
9 7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	194 <test>
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	195 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData"/>
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	196 <expand macro="test_annotate_diffreport"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	197 <expand macro="test_annotate_quick_true"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	198 <expand macro="test_file_load_zip"/>
9 7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	199 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" />
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	200 <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" />
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	201 </test>
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	202 <test>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	203 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	204 <expand macro="test_annotate_diffreport"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	205 <expand macro="test_annotate_quick_true"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	206 <expand macro="test_file_load_single"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	207 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	208 <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	209 </test>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	210 <test>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	211 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	212 <expand macro="test_annotate_diffreport"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	213 <conditional name="quick_block">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	214 <expand macro="test_annotate_quick_false" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	215 <section name="findadducts">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	216 <param name="polarity" value="negative"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	217 <conditional name="rules_block">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	218 <param name="rules_select" value="TRUE"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	219 <param name="rules" value="CASMI_extended_NEG_rules.csv" ftype="csv"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	220 </conditional>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	221 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	222 </conditional>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	223 <expand macro="test_file_load_single"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	224 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	225 <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.dataMatrix.tsv" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	226 </test>
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	227 </tests>
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	228
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	229
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	230
8 8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	231 <help><![CDATA[
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	232
9 7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	233 @HELP_AUTHORS@
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	234
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	235 ================
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	236 CAMERA.annotate
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	237 ================
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	238
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	239 -----------
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	240 Description
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	241 -----------
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	242
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	243 The R-package CAMERA is a Collection of Algorithms for MEtabolite
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	244 pRofile Annotation. Its primary purpose is the annotation and evaluation of
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	245 LC-MS data. It includes algorithms for annotation of isotope peaks, adducts
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	246 and fragments in peak lists. Additional methods cluster mass signals that
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	247 originate from a single metabolite, based on rules for mass differences and
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	248 peak shape comparison. To use the strength of already existing programs,
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	249 CAMERA is designed to interact directly with processed peak data from the
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	250 R-package xcms.
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	251
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	252 What it does?
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	253
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	254 The CAMERA annotation procedure can be split into two parts: We want to answer the questions which peaks occur from the same molecule and secondly compute its exact mass and annotate the ion species. Therefore CAMERA annotation workflow contains following primary functions: 1. peak grouping after retention time (groupFWHM) 2. peak group verification with peakshape correlation (groupCorr) Both methods separate peaks into different groups, which we define as ”pseu- dospectra”. Those pseudospectra can consists from one up to 100 ions, de- pending on the molecules amount and ionizability. Afterwards the exposure of the ion species can be performed with: 2 1. annotation of possible isotopes (findIsotopes) 2. annotation of adducts and calculating hypothetical masses for the group (findAdducts) This workflow results in a data-frame similar to a xcms peak table, that can be easily stored in a comma separated table .csv (Excel-readable).
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	255
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	256 If you have two or more conditions, it will return a diffreport result within the annotation results.
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	257 The diffreport result shows the most significant differences between two sets of samples. Optionally
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	258 create extracted ion chromatograms for the most significant differences.
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	259
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	260
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	261 -----------------
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	262 Workflow position
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	263 -----------------
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	264
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	265
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	266 Upstream tools
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	267
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	268 ========================= ==================== ====================== ==========
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	269 Name output file format parameter
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	270 ========================= ==================== ====================== ==========
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	271 xcms.fillPeaks xset.fillPeaks.RData rdata.xcms.fillpeaks RData file
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	272 ========================= ==================== ====================== ==========
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	273
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	274
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	275 Downstream tools
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	276
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	277 +---------------------------+---------------------------------------+------------------------------------------------+
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	278 \| Name \| Output file \| Format \|
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	279 +===========================+=======================================+================================================+
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	280 \|CAMERA_combinexsAnnot \|xset.annotate.Rdata \| rdata.camera.positive or rdata.camera.negative \|
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	281 +---------------------------+---------------------------------------+------------------------------------------------+
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	282 \|Determine Vdk or Lowess \|xset.annotate.dataMatrix.tsv \| Tabular \|
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	283 +---------------------------+---------------------------------------+------------------------------------------------+
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	284 \|Normalization Vdk/Lowess \|xset.annotate.dataMatrix.tsv \| Tabular \|
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	285 +---------------------------+---------------------------------------+------------------------------------------------+
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	286 \|Anova \|xset.annotate.dataMatrix.tsv \| Tabular \|
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	287 +---------------------------+---------------------------------------+------------------------------------------------+
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	288 \|PCA \|xset.annotate.dataMatrix.tsv \| Tabular \|
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	289 +---------------------------+---------------------------------------+------------------------------------------------+
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	290 \|Hierarchical Clustering \|xset.annotate.dataMatrix.tsv \| Tabular \|
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	291 +---------------------------+---------------------------------------+------------------------------------------------+
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	292
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	293
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	294 The output file xset.annotate.dataMatrix.tsv is an tabular file. You can continue your analysis using it in the following tools:
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	295
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	296 \| Determine Vdk or Lowess
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	297 \| Normalization Vdk/Lowess
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	298 \| Anova
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	299 \| PCA
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	300 \| Hierarchical Clustering
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	301
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	302
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	303 General schema of the metabolomic workflow
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	304
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	305 .. image:: annotate_workflow.png
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	306
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	307 -----------
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	308 Input files
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	309 -----------
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	310
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	311 +---------------------------+---------------------------+
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	312 \| Parameter : num + label \| Format \|
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	313 +===========================+===========================+
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	314 \| 1 : RData file \| rdata.xcms.fillpeaks \|
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	315 +---------------------------+---------------------------+
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	316
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	317
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	318 [Optional] User defined ruleset:
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	319 --------------------------------
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	320
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	321 Example:
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	322
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	323 \| "name","nmol","charge","massdiff","oidscore","quasi","ips"
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	324 \| "[M-H]-",1,-1,-1.007276,1,1,1
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	325 \| "[M-2H]2-",1,-2,-2.014552,2,0,1
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	326 \| "[M-3H]3-",1,-3,-3.021828,3,0,1
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	327 \| "[M-2H+Na]-",1,-1,20.974666,4,0,0.25
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	328 \| "[M-H+Cl]2-",1,-2,33.962126,5,0,1
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	329 \| "[M-2H+K]-",1,-1,36.948606,6,0,0.25
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	330 \| "[M+Cl]-",1,-1,34.969402,7,1,1
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	331 \| "[M+2Cl]2-",1,-2,69.938804,8,0,1
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	332 \| "[2M-H]-",2,-1,-1.007276,1,0,0.5
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	333
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	334 ----------
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	335 Parameters
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	336 ----------
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	337
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	338 diffreport: Intensity values to be used for the diffreport
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	339 ----------------------------------------------------------
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	340
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	341 \| If value="into", integrated peak intensities are used.
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	342 \| If value="maxo", maximum peak intensities are used.
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	343 \| If value="intb", baseline corrected integrated peak intensities are used (only available if peak detection was done by ‘findPeaks.centWave’).
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	344
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	345
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	346
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	347 ------------
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	348 Output files
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	349 ------------
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	350
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	351 xset.annotate.variableMetadata.tsv
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	352
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	353 \| For each metabolite (row) :
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	354 \| the value of the intensity in each sample, fold, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct and pcgroup
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	355
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	356 xset.annotate.dataMatrix.tsv
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	357
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	358 \| A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column).
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	359
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	360 xset.annotate.zip
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	361
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	362 \| It contains filebase_eic, filebase_box and filebase.tsv for one conditon vs another (Anova analysis).
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	363
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	364 xset.annotate.Rdata rdata.camera.quick or rdata.camera.positive or rdata.camera.negative
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	365
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	366 \| Rdata file, that be used outside Galaxy in R.
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	367
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	368 ------
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	369
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	370 .. class:: infomark
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	371
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	372 The output "xset.annotate.dataMatrix.tsv" is a tabular file. You can continue your analysis using it in the following tools of the workflow:
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	373
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	374 \| Determine Vdk or Lowess (Data correction)
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	375 \| Normalization Vdk/Lowess (Data correction)
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	376 \| Anova (Statistical analysis)
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	377 \| PCA (Statistical analysis)
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	378 \| Hierarchical Clustering (Statistical analysis)
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	379
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	380
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	381 ---------------------------------------------------
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	382
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	383 ---------------
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	384 Working example
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	385 ---------------
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	386
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	387 Input files
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	388 -----------
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	389
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	390 \| RData file -> xset.fillPeaks.RData
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	391
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	392 Parameters
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	393 ----------
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	394
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	395 \| sortpval -> false
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	396 \| sigma -> 6 (default)
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	397 \| perfwhm -> 0.6 (default)
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	398 \| maxcharge -> 3 (default)
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	399 \| maxiso -> 4 (default)
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	400 \| minfrac -> 0.5 (default)
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	401 \| ppm -> 500
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	402 \| mzabs -> 0.015(default)
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	403 \| Advanced options -> hide
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	404 \| Numver of condition -> Two or more conditioons
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	405 \| eicmax -> 200
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	406 \| eicwidth -> 200 (default)
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	407
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	408
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	409
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	410 Output files
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	411 ------------
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	412
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	413 Example of an xset.annotate.dataMatrix.tsv output
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	414
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	415 .. image:: annotatediffreport_dataMatrix.png
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	416
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	417 Example of a part of xset.annotate.variableMetadata.tsv output
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	418
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	419 .. image:: annotatediffreport_variableMetadata.png
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	420
8 8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	421
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	422 ---------------------------------------------------
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	423
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	424 Changelog/News
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	425 --------------
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	426
15 6139bfcc95cb planemo upload commit 98f8d5d3e1a4356b411f16644ffa4da444ac2bdb lecorguille parents: 14 diff changeset	427 Version 2.2.2 - 01/03/2018
6139bfcc95cb planemo upload commit 98f8d5d3e1a4356b411f16644ffa4da444ac2bdb lecorguille parents: 14 diff changeset	428
6139bfcc95cb planemo upload commit 98f8d5d3e1a4356b411f16644ffa4da444ac2bdb lecorguille parents: 14 diff changeset	429 - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0
6139bfcc95cb planemo upload commit 98f8d5d3e1a4356b411f16644ffa4da444ac2bdb lecorguille parents: 14 diff changeset	430
14 225cb8347572 planemo upload commit 239d7043ccba9d1d1861d7d8ac353c77497e0880 lecorguille parents: 13 diff changeset	431 Version 2.2.1 - 29/11/2017
225cb8347572 planemo upload commit 239d7043ccba9d1d1861d7d8ac353c77497e0880 lecorguille parents: 13 diff changeset	432
225cb8347572 planemo upload commit 239d7043ccba9d1d1861d7d8ac353c77497e0880 lecorguille parents: 13 diff changeset	433 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
225cb8347572 planemo upload commit 239d7043ccba9d1d1861d7d8ac353c77497e0880 lecorguille parents: 13 diff changeset	434
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	435 Version 2.2.0 - 28/03/2017
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	436
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	437 - BUGFIX: the diffreport ids didn't convert the rt in minute as the other export
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	438
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	439 - UPDATE: the settings (digits, convertion in minutes) of the identifiants will no longer modify the native one. Because we want to be conservative and because it can be dangerous for the data integrity during a futur merge of the table, we decide to put those customization in a new column namecustom within the variableMetadata.
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	440
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	441 - IMPROVEMENT: add some sections within to separate the different parts of the process
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	442
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	443 - IMPROVEMENT: add the possibility to use defined ruleset
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	444
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	445 - IMPROVEMENT: add the possibility to set the MZ digit within the identifiants
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	446
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	447 - IMPROVEMENT: CAMERA.annotate is now compatible with merged individual data from xcms.xcmsSet
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	448
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	449
9 7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	450 Version 2.1.5 - 21/04/2016
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	451
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	452 - UPGRADE: upgrade the CAMERA version from 1.22.0 to 1.26.0
9 7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	453
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	454
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	455 Version 2.1.4 - 18/04/2016
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	456
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	457 - TEST: refactoring to pass planemo test using conda dependencies
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	458
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	459
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	460 Version 2.1.3 - 10/02/2016
8 8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	461
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	462 - BUGFIX: better management of errors. Datasets remained green although the process failed
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	463
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	464 - BUGFIX: the conversion into minutes of the retention time was applied to the diffreport outputs (several conditions)
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	465
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	466 - IMPROVEMENT: when there are several conditions, the tool will generate individual datasets (tsv, pdf) instead of a zip file. The usual png (eic, boxplot) will from now be integrated in two pdf.
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	467
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	468 - UPDATE: refactoring of internal management of inputs/outputs
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	469
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	470
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	471 VERSION 2.1.0 - 09/10/2015
8 8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	472
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	473 - BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don't match with the metabolites))
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	474
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	475
13 1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419 lecorguille parents: 10 diff changeset	476 VERSION 2.1.0 - 07/06/2015
8 8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	477
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	478 - IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors.
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	479
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	480 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	481
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	482 - UPDATE: merged with annotateDiffreport. Some parameters are dedicated to experiences with several conditions
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	483
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	484
8c5bb7b86df9 planemo upload lecorguille parents: 5 diff changeset	485 ]]></help>
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	486
9 7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b lecorguille parents: 8 diff changeset	487 <expand macro="citation" />
0 e0afb8854cc4 planemo upload lecorguille parents: diff changeset	488
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	489
e0afb8854cc4 planemo upload lecorguille parents: diff changeset	490 </tool>

Mercurial > repos > lecorguille > camera_annotate

annotate abims_CAMERA_annotateDiffreport.xml @ 15:6139bfcc95cb draft