annotate abims_CAMERA_annotateDiffreport.xml @ 24:512c2b701d96 draft

"planemo upload commit 8c20c85850fa44e3ac0f560f2269e86a51b9ebf0"
author workflow4metabolomics
date Fri, 02 Jul 2021 02:51:41 +0000
parents abf1775ac14d
children 4b9ab71be05e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
23
abf1775ac14d "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998"
workflow4metabolomics
parents: 22
diff changeset
1 <tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.6+camera@TOOL_VERSION@-galaxy0">
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[
18
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
13 @COMMAND_RSCRIPT@/CAMERA_annotateDiffreport.r
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
14 image '$image'
8
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
15
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
16 nSlaves \${GALAXY_SLOTS:-1}
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
17
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
18 ## groupFWHM
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
19 sigma $groupfwhm.sigma
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
20 perfwhm $groupfwhm.perfwhm
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
21
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
22 ## findGeneral
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
23 ppm $findgeneral.ppm
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
24 mzabs $findgeneral.mzabs
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
25
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
26 ## findIsotopes
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
27 maxcharge $findisotopes.maxcharge
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
28 maxiso $findisotopes.maxiso
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
29 minfrac $findisotopes.minfrac
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
30
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
31 quick $quick_block.quick
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
32 #if $quick_block.quick == "FALSE":
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
33 ## groupcorr
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
34 cor_eic_th $quick_block.groupcorr.cor_eic_th
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
35 graphMethod $quick_block.groupcorr.graphMethod
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
36 pval $quick_block.groupcorr.pval
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
37 calcCiS $quick_block.groupcorr.calcCiS
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
38 calcIso $quick_block.groupcorr.calcIso
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
39 calcCaS $quick_block.groupcorr.calcCaS
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
40
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
41 ## findadducts
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
42 polarity $quick_block.findadducts.polarity
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
43 max_peaks $quick_block.findadducts.max_peaks
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
44 #if $quick_block.findadducts.rules_block.rules_select == "FALSE":
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
45 multiplier $quick_block.findadducts.rules_block.multiplier
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
46 #else
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
47 rules $quick_block.findadducts.rules_block.rules
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
48 #end if
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
49 #end if
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
50
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
51 #if $diffreport.options.option == "show":
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
52 ## diffreport
8
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
53 runDiffreport TRUE
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
54 eicmax $diffreport.options.eicmax
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
55 eicwidth $diffreport.options.eicwidth
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
56 value $diffreport.options.value
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
57 sortpval $diffreport.options.sortpval
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
58 h $diffreport.options.h
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
59 w $diffreport.options.w
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
60 mzdec $diffreport.options.mzdec
18
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
61 tabular2 $diffreport.options.tabular2
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
62 png2 $diffreport.options.png2
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
63 #end if
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
64
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
65 @COMMAND_PEAKLIST@
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
66
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
67 @COMMAND_FILE_LOAD@
9
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 8
diff changeset
68
8
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
69 ]]></command>
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
70
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
71 <inputs>
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
72
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
73
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
74 <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
75
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
76 <section name="groupfwhm" title="Group co-eluted peaks based on RT [groupFWHM]" expanded="True">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
77 <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
78 <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
79 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
80
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
81 <section name="findgeneral" title="Annotation general options" expanded="True">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
82 <param name="ppm" type="integer" value="5" label="General ppm error" help="[ppm]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
83 <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
84 </section>
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
85
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
86 <section name="findisotopes" title="Annotate Isotopes [findIsotopes]" expanded="True">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
87 <param name="maxcharge" type="integer" value="3" label="Max. ion charge" help="[maxcharge]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
88 <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
89 <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
90 </section>
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
91
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
92 <conditional name="quick_block">
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
93 <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
94 <option value="FALSE" selected="true">All functions</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
95 <option value="TRUE">Only groupFWHM and findIsotopes functions [quick]</option>
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
96 </param>
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
97 <when value="FALSE">
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
98
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
99 <section name="groupcorr" title="Verifying grouping co-eluted peaks [groupCorr]" expanded="True">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
100 <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
101 <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
102 <option value="hcs" selected="true">hcs</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
103 <option value="lpc">lpc</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
104 </param>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
105 <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
106 <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
107 <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
108 <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
109 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
110
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
111 <section name="findadducts" title="Annotate Adducts [findAdducts]" expanded="True">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
112 <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
113 <option value="positive" >positive</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
114 <option value="negative" selected="true">negative</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
115 </param>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
116 <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
117 <conditional name="rules_block">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
118 <param name="rules_select" type="select" label="Use a personal ruleset file">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
119 <option value="TRUE">TRUE</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
120 <option value="FALSE" selected="true">FALSE</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
121 </param>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
122 <when value="FALSE">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
123 <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
124 </when>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
125 <when value="TRUE">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
126 <param name="rules" type="data" format="csv" label="User defined ruleset" help="[rules]" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
127 </when>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
128 </conditional>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
129 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
130
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">
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
133 <param name="polarity" type="hidden" value="quick" label="for the output label" help="for the output label" />
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
134 </when>
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
135 </conditional>
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
136
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
137 <!-- Diffreport specific parameters -->
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
138 <section name="diffreport" title="Statistics and results export: [diffreport]" expanded="True">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
139 <conditional name="options">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
140 <param name="option" type="select" label="Number of condition">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
141 <option value="hide" selected="true">One condition</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
142 <option value="show">Two or more conditions</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
143 </param>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
144 <when value="show">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
145 <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
146 <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
147 <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
148 <option value="into" selected="true">into</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
149 <option value="maxo" >maxo</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
150 <option value="intb">intb</option>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
151 </param>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
152 <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
153 <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
154 <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
155 <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]"/>
18
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
156 <param name="tabular2" type="select" label="Export the Diffreport files in ">
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
157 <option value="zip" selected="true">Zip</option>
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
158 <option value="datasetcollection">Individual file in a Dataset Collection</option>
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
159 </param>
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
160 <param name="png2" type="select" label="Export the EIC and boxplots in ">
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
161 <option value="zip" selected="true">Zip</option>
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
162 <option value="pdf">Individual pdf</option>
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
163 </param>
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
164 </when>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
165 <when value="hide">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
166 </when>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
167 </conditional>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
168 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
169
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
170 <expand macro="input_peaklist"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
171 <expand macro="input_file_load"/>
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
172 </inputs>
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
173
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
174 <outputs>
18
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
175 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
176 <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata" from_work_dir="annotatediff.RData">
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
177 <filter>quick_block['quick'] == 'FALSE'</filter>
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
178 <change_format>
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
179 <when input="quick_block.findadducts.polarity" value="positive" format="rdata.camera.positive" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
180 <when input="quick_block.findadducts.polarity" value="negative" format="rdata.camera.negative" />
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
181 </change_format>
3
729991209550 Uploaded
mmonsoor
parents: 0
diff changeset
182 </data>
18
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
183 <data name="rdata_quick_true" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.quick.Rdata" from_work_dir="annotatediff.RData">
13
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>
18
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
186
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
187 <data name="output_diffreport_eic_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_eic.zip" from_work_dir="eic.zip" >
20
b979ba5888f7 "planemo upload commit 0b77855ab98a4940d58727271c28990969367f4d"
workflow4metabolomics
parents: 19
diff changeset
188 <filter>diffreport['options']['option'] == 'show' and diffreport['options']['eicmax'] > 0 and diffreport['options']['png2'] == 'zip'</filter>
18
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
189 </data>
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
190 <data name="output_diffreport_box_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_box.zip" from_work_dir="box.zip" >
20
b979ba5888f7 "planemo upload commit 0b77855ab98a4940d58727271c28990969367f4d"
workflow4metabolomics
parents: 19
diff changeset
191 <filter>diffreport['options']['option'] == 'show' and diffreport['options']['eicmax'] > 0 and diffreport['options']['png2'] == 'zip'</filter>
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
192 </data>
18
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
193 <collection name="output_diffreport_picture_pdf" type="list" label="${image.name[:-6]}.annotateDiffreport.pdf">
20
b979ba5888f7 "planemo upload commit 0b77855ab98a4940d58727271c28990969367f4d"
workflow4metabolomics
parents: 19
diff changeset
194 <filter>diffreport['options']['option'] == 'show' and diffreport['options']['eicmax'] > 0 and diffreport['options']['png2'] == 'pdf'</filter>
18
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
195 <discover_datasets pattern="__designation_and_ext__" directory="pdf" format="pdf" />
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
196 </collection>
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
197
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
198 <data name="output_diffreport_table_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_table.zip" from_work_dir="tabular.zip">
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
199 <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'zip'</filter>
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
200 </data>
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
201 <collection name="output_diffreport_table_collection" type="list" label="${image.name[:-6]}.annotateDiffreport_table">
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
202 <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'datasetcollection'</filter>
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
203 <discover_datasets pattern="__designation_and_ext__" directory="tabular" format="tabular" />
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
204 </collection>
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
205 </outputs>
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
206
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
207 <tests>
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
208 <test>
23
abf1775ac14d "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998"
workflow4metabolomics
parents: 22
diff changeset
209 <param name="image" value="faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.RData"/>
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
210 <expand macro="test_annotate_diffreport"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
211 <expand macro="test_annotate_quick_true"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
212 <expand macro="test_file_load_single"/>
17
73d82de36369 planemo upload commit 1a5357c0e28103a0325b2df858504721f6266049
lecorguille
parents: 16
diff changeset
213 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" lines_diff="2" />
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
214 </test>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
215 <test>
23
abf1775ac14d "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998"
workflow4metabolomics
parents: 22
diff changeset
216 <param name="image" value="faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.RData"/>
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
217 <expand macro="test_annotate_diffreport"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
218 <conditional name="quick_block">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
219 <expand macro="test_annotate_quick_false" />
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
220 <section name="findadducts">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
221 <param name="polarity" value="negative"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
222 <conditional name="rules_block">
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
223 <param name="rules_select" value="TRUE"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
224 <param name="rules" value="CASMI_extended_NEG_rules.csv" ftype="csv"/>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
225 </conditional>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
226 </section>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
227 </conditional>
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
228 <expand macro="test_file_load_single"/>
17
73d82de36369 planemo upload commit 1a5357c0e28103a0325b2df858504721f6266049
lecorguille
parents: 16
diff changeset
229 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv" lines_diff="2"/>
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
230 </test>
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
231 </tests>
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
232
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
233
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
234
8
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
235 <help><![CDATA[
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
236
9
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 8
diff changeset
237 @HELP_AUTHORS@
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
238
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
239 ================
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
240 CAMERA.annotate
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
241 ================
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
242
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
243 -----------
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
244 Description
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
245 -----------
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
246
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
247 The R-package CAMERA is a Collection of Algorithms for MEtabolite
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
248 pRofile Annotation. Its primary purpose is the annotation and evaluation of
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
249 LC-MS data. It includes algorithms for annotation of isotope peaks, adducts
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
250 and fragments in peak lists. Additional methods cluster mass signals that
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
251 originate from a single metabolite, based on rules for mass differences and
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
252 peak shape comparison. To use the strength of already existing programs,
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
253 CAMERA is designed to interact directly with processed peak data from the
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
254 R-package **xcms**.
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
255
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
256 **What it does?**
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
257
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
258 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
259
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
260 If you have two or more conditions, it will return a diffreport result within the annotation results.
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
261 The diffreport result shows the most significant differences between two sets of samples. Optionally
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
262 create extracted ion chromatograms for the most significant differences.
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 Workflow position
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
267 -----------------
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
268
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
269
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
270 **Upstream tools**
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
271
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
272 ========================= ==================== ====================== ==========
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
273 Name output file format parameter
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
274 ========================= ==================== ====================== ==========
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
275 xcms.fillPeaks xset.fillPeaks.RData rdata.xcms.fillpeaks RData file
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
276 ========================= ==================== ====================== ==========
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
277
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
278
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
279 **Downstream tools**
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
280
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
281 +---------------------------+---------------------------------------+------------------------------------------------+
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
282 | Name | Output file | Format |
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
283 +===========================+=======================================+================================================+
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
284 |CAMERA_combinexsAnnot |xset.annotate.Rdata | rdata.camera.positive or rdata.camera.negative |
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
285 +---------------------------+---------------------------------------+------------------------------------------------+
17
73d82de36369 planemo upload commit 1a5357c0e28103a0325b2df858504721f6266049
lecorguille
parents: 16
diff changeset
286 |Determine Vdk or Lowess |xset.annotate.variableMetadata.tsv | Tabular |
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
287 +---------------------------+---------------------------------------+------------------------------------------------+
17
73d82de36369 planemo upload commit 1a5357c0e28103a0325b2df858504721f6266049
lecorguille
parents: 16
diff changeset
288 |Normalization Vdk/Lowess |xset.annotate.variableMetadata.tsv | Tabular |
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
289 +---------------------------+---------------------------------------+------------------------------------------------+
17
73d82de36369 planemo upload commit 1a5357c0e28103a0325b2df858504721f6266049
lecorguille
parents: 16
diff changeset
290 |Anova |xset.annotate.variableMetadata.tsv | Tabular |
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
291 +---------------------------+---------------------------------------+------------------------------------------------+
17
73d82de36369 planemo upload commit 1a5357c0e28103a0325b2df858504721f6266049
lecorguille
parents: 16
diff changeset
292 |PCA |xset.annotate.variableMetadata.tsv | Tabular |
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
293 +---------------------------+---------------------------------------+------------------------------------------------+
17
73d82de36369 planemo upload commit 1a5357c0e28103a0325b2df858504721f6266049
lecorguille
parents: 16
diff changeset
294 |Hierarchical Clustering |xset.annotate.variableMetadata.tsv | Tabular |
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
295 +---------------------------+---------------------------------------+------------------------------------------------+
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
296
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
297
17
73d82de36369 planemo upload commit 1a5357c0e28103a0325b2df858504721f6266049
lecorguille
parents: 16
diff changeset
298 The output file **xset.annotate.variableMetadata.tsv** is an tabular file. You can continue your analysis using it in the following tools:
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
299
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
300 | Determine Vdk or Lowess
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
301 | Normalization Vdk/Lowess
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
302 | Anova
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
303 | PCA
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
304 | Hierarchical Clustering
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
305
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
306
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
307 **General schema of the metabolomic workflow**
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
308
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
309 .. image:: annotate_workflow.png
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
310
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
311 -----------
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
312 Input files
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
313 -----------
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
314
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
315 +---------------------------+---------------------------+
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
316 | Parameter : num + label | Format |
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
317 +===========================+===========================+
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
318 | 1 : RData file | rdata.xcms.fillpeaks |
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
319 +---------------------------+---------------------------+
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
320
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
321
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
322 [Optional] User defined ruleset:
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
323 --------------------------------
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
324
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
325 Example:
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
326
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
327 | "name","nmol","charge","massdiff","oidscore","quasi","ips"
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
328 | "[M-H]-",1,-1,-1.007276,1,1,1
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
329 | "[M-2H]2-",1,-2,-2.014552,2,0,1
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
330 | "[M-3H]3-",1,-3,-3.021828,3,0,1
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
331 | "[M-2H+Na]-",1,-1,20.974666,4,0,0.25
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
332 | "[M-H+Cl]2-",1,-2,33.962126,5,0,1
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
333 | "[M-2H+K]-",1,-1,36.948606,6,0,0.25
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
334 | "[M+Cl]-",1,-1,34.969402,7,1,1
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
335 | "[M+2Cl]2-",1,-2,69.938804,8,0,1
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
336 | "[2M-H]-",2,-1,-1.007276,1,0,0.5
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
337
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
338 ----------
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
339 Parameters
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
340 ----------
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
341
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
342 diffreport: Intensity values to be used for the diffreport
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
343 ----------------------------------------------------------
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
344
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
345 | If **value="into"**, integrated peak intensities are used.
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
346 | If **value="maxo"**, maximum peak intensities are used.
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
347 | 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
348
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
349
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
350
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
351 ------------
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
352 Output files
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
353 ------------
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
354
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
355 xset.annotate.variableMetadata.tsv
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
356
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
357 | For each metabolite (row) :
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
358 | 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
359
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
17
73d82de36369 planemo upload commit 1a5357c0e28103a0325b2df858504721f6266049
lecorguille
parents: 16
diff changeset
372 The output **"xset.annotate.variableMetadata.tsv"** is a tabular file. You can continue your analysis using it in the following tools of the workflow:
0
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
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
413 **Example of a part of xset.annotate.variableMetadata.tsv output**
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
414
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
415 .. image:: annotatediffreport_variableMetadata.png
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
416
8
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
417
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
418 ---------------------------------------------------
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
419
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
420 Changelog/News
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
421 --------------
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
422
18
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
423 .. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
424
24
512c2b701d96 "planemo upload commit 8c20c85850fa44e3ac0f560f2269e86a51b9ebf0"
workflow4metabolomics
parents: 23
diff changeset
425 @HELP_CAMERA_NEWVERSION_1480@
512c2b701d96 "planemo upload commit 8c20c85850fa44e3ac0f560f2269e86a51b9ebf0"
workflow4metabolomics
parents: 23
diff changeset
426
23
abf1775ac14d "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998"
workflow4metabolomics
parents: 22
diff changeset
427 @HELP_CAMERA_NEWVERSION_1460@
abf1775ac14d "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998"
workflow4metabolomics
parents: 22
diff changeset
428
22
01bbba6d57ff "planemo upload commit e363c270e2f9d72cb0ede1a7f3bc61418b72c4c4"
workflow4metabolomics
parents: 21
diff changeset
429 **Version 2.2.6+camera1.42.0-galaxy1 - 09/03/2020**
20
b979ba5888f7 "planemo upload commit 0b77855ab98a4940d58727271c28990969367f4d"
workflow4metabolomics
parents: 19
diff changeset
430
b979ba5888f7 "planemo upload commit 0b77855ab98a4940d58727271c28990969367f4d"
workflow4metabolomics
parents: 19
diff changeset
431 - BUGFIX: Fix the zip export of the pictures (eic and boxplot)
b979ba5888f7 "planemo upload commit 0b77855ab98a4940d58727271c28990969367f4d"
workflow4metabolomics
parents: 19
diff changeset
432
19
01459b73daf9 "planemo upload commit 4fcbbcbc6d6b0a59e801870d31fe886a920ef429"
workflow4metabolomics
parents: 18
diff changeset
433 @HELP_CAMERA_NEWVERSION_1420@
01459b73daf9 "planemo upload commit 4fcbbcbc6d6b0a59e801870d31fe886a920ef429"
workflow4metabolomics
parents: 18
diff changeset
434
18
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
435 **Version 2.2.5 - 09/04/2019**
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
436
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
437 - NEW: zip export are back for pictures (eic and boxplot) and diffreport tables
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
438
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
439 - UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_)
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
440
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
441 - UPGRADE: refactoring of internal code
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
442
17
73d82de36369 planemo upload commit 1a5357c0e28103a0325b2df858504721f6266049
lecorguille
parents: 16
diff changeset
443 **Version 2.2.4 - 09/10/2018**
73d82de36369 planemo upload commit 1a5357c0e28103a0325b2df858504721f6266049
lecorguille
parents: 16
diff changeset
444
18
cb923396e70f planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
lecorguille
parents: 17
diff changeset
445 - NEW: CAMERA.annotate no longer export a DataMatrix. fillChromPeaks does the job
17
73d82de36369 planemo upload commit 1a5357c0e28103a0325b2df858504721f6266049
lecorguille
parents: 16
diff changeset
446
16
a2c49996603e planemo upload commit e440674afa3e58c46100b0ac7c305a6f46ecbbdc
lecorguille
parents: 15
diff changeset
447 **Version 2.2.3 - 30/04/2018**
a2c49996603e planemo upload commit e440674afa3e58c46100b0ac7c305a6f46ecbbdc
lecorguille
parents: 15
diff changeset
448
a2c49996603e planemo upload commit e440674afa3e58c46100b0ac7c305a6f46ecbbdc
lecorguille
parents: 15
diff changeset
449 - NEW: support the new xcms 3.0.0 wrapper
a2c49996603e planemo upload commit e440674afa3e58c46100b0ac7c305a6f46ecbbdc
lecorguille
parents: 15
diff changeset
450
15
6139bfcc95cb planemo upload commit 98f8d5d3e1a4356b411f16644ffa4da444ac2bdb
lecorguille
parents: 14
diff changeset
451 **Version 2.2.2 - 01/03/2018**
6139bfcc95cb planemo upload commit 98f8d5d3e1a4356b411f16644ffa4da444ac2bdb
lecorguille
parents: 14
diff changeset
452
6139bfcc95cb planemo upload commit 98f8d5d3e1a4356b411f16644ffa4da444ac2bdb
lecorguille
parents: 14
diff changeset
453 - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0
6139bfcc95cb planemo upload commit 98f8d5d3e1a4356b411f16644ffa4da444ac2bdb
lecorguille
parents: 14
diff changeset
454
14
225cb8347572 planemo upload commit 239d7043ccba9d1d1861d7d8ac353c77497e0880
lecorguille
parents: 13
diff changeset
455 **Version 2.2.1 - 29/11/2017**
225cb8347572 planemo upload commit 239d7043ccba9d1d1861d7d8ac353c77497e0880
lecorguille
parents: 13
diff changeset
456
225cb8347572 planemo upload commit 239d7043ccba9d1d1861d7d8ac353c77497e0880
lecorguille
parents: 13
diff changeset
457 - 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
458
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
459 **Version 2.2.0 - 28/03/2017**
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
460
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
461 - 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
462
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
463 - 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
464
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
465 - IMPROVEMENT: add some sections within to separate the different parts of the process
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
466
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
467 - IMPROVEMENT: add the possibility to use defined ruleset
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
468
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
469 - IMPROVEMENT: add the possibility to set the MZ digit within the identifiants
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
470
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
471 - IMPROVEMENT: CAMERA.annotate is now compatible with merged individual data from xcms.xcmsSet
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
472
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
473
9
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 8
diff changeset
474 **Version 2.1.5 - 21/04/2016**
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 8
diff changeset
475
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
476 - UPGRADE: upgrade the CAMERA version from 1.22.0 to 1.26.0
9
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 8
diff changeset
477
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 8
diff changeset
478
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 8
diff changeset
479 **Version 2.1.4 - 18/04/2016**
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 8
diff changeset
480
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 8
diff changeset
481 - TEST: refactoring to pass planemo test using conda dependencies
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 8
diff changeset
482
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 8
diff changeset
483
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 8
diff changeset
484 **Version 2.1.3 - 10/02/2016**
8
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
485
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
486 - BUGFIX: better management of errors. Datasets remained green although the process failed
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
487
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
488 - 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
489
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
490 - 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
491
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
492 - UPDATE: refactoring of internal management of inputs/outputs
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
493
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
494
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
495 **VERSION 2.1.0 - 09/10/2015**
8
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
496
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
497 - 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
498
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
499
13
1c30ff90f3ae planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
lecorguille
parents: 10
diff changeset
500 **VERSION 2.1.0 - 07/06/2015**
8
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
501
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
502 - 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
503
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
504 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
505
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
506 - UPDATE: merged with annotateDiffreport. Some parameters are dedicated to experiences with several conditions
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
507
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
508
8c5bb7b86df9 planemo upload
lecorguille
parents: 5
diff changeset
509 ]]></help>
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
510
9
7da9252dd983 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 8
diff changeset
511 <expand macro="citation" />
0
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
512
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
513
e0afb8854cc4 planemo upload
lecorguille
parents:
diff changeset
514 </tool>