Mercurial > repos > lecorguille > camera_annotate

annotate abims_CAMERA_annotateDiffreport.xml @ 46:67f0ef6236f1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit a923a432239a1f2ffee2dae1281fe2d8f41bac38
author workflow4metabolomics
date Mon, 30 Sep 2024 12:21:23 +0000
parents db77f2b67a7f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
46
67f0ef6236f1 planemo upload commit a923a432239a1f2ffee2dae1281fe2d8f41bac38
workflow4metabolomics
parents: 45
diff changeset
1 <tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.7+camera@TOOL_VERSION@-galaxy@VERSION_SUFFIX@">
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
2
b495191430d5 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>
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
4
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 6
diff changeset
5 <macros>
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 6
diff changeset
6 <import>macros.xml</import>
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 6
diff changeset
7 </macros>
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 6
diff changeset
8
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 6
diff changeset
9 <expand macro="requirements"/>
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 6
diff changeset
10 <expand macro="stdio"/>
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
11
1
a887bff50e45 Uploaded
lecorguille
parents: 0
diff changeset
12 <command><![CDATA[
39
db9bc2c27a0a planemo upload commit d51a0d0a26833671b79711ee18d782e84f301e76
workflow4metabolomics
parents: 38
diff changeset
13 @COMMAND_RSCRIPT@/CAMERA_annotateDiffreport.r
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
14 image '$image'
1
a887bff50e45 Uploaded
lecorguille
parents: 0
diff changeset
15
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
16 nSlaves \${GALAXY_SLOTS:-1}
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
17
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
18 ## groupFWHM
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
19 sigma $groupfwhm.sigma
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
20 perfwhm $groupfwhm.perfwhm
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
21
30
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
22 ## findGeneral
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
23 ppm $findgeneral.ppm
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
24 mzabs $findgeneral.mzabs
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
25
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
26 ## findIsotopes
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
27 maxcharge $findisotopes.maxcharge
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
28 maxiso $findisotopes.maxiso
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
29 minfrac $findisotopes.minfrac
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
30
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
31 quick $quick_block.quick
30
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
32 #if $quick_block.quick == "FALSE":
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
33 ## groupcorr
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
34 cor_eic_th $quick_block.groupcorr.cor_eic_th
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
35 graphMethod $quick_block.groupcorr.graphMethod
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
36 pval $quick_block.groupcorr.pval
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
37 calcCiS $quick_block.groupcorr.calcCiS
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
38 calcIso $quick_block.groupcorr.calcIso
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
39 calcCaS $quick_block.groupcorr.calcCaS
30
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
40
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
41 ## findadducts
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
42 polarity $quick_block.findadducts.polarity
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
43 max_peaks $quick_block.findadducts.max_peaks
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
44 #if $quick_block.findadducts.rules_block.rules_select == "FALSE":
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
45 multiplier $quick_block.findadducts.rules_block.multiplier
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
46 #else
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
47 rules $quick_block.findadducts.rules_block.rules
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
48 #end if
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
49 #end if
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
50
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
51 #if $diffreport.options.option == "show":
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
52 ## diffreport
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
53 runDiffreport TRUE
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
54 eicmax $diffreport.options.eicmax
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
55 eicwidth $diffreport.options.eicwidth
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
56 value $diffreport.options.value
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
57 sortpval $diffreport.options.sortpval
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
58 h $diffreport.options.h
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
59 w $diffreport.options.w
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
60 mzdec $diffreport.options.mzdec
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
61 tabular2 $diffreport.options.tabular2
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
62 png2 $diffreport.options.png2
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
63 #end if
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
64
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
65 @COMMAND_PEAKLIST@
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
66
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
67 @COMMAND_FILE_LOAD@
11
d33e0ed5f32a planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835-dirty
lecorguille
parents: 9
diff changeset
68
1
a887bff50e45 Uploaded
lecorguille
parents: 0
diff changeset
69 ]]></command>
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
70
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
71 <inputs>
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
72
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
73
0
b495191430d5 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)" />
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
75
30
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
76 <section name="groupfwhm" title="Group co-eluted peaks based on RT [groupFWHM]" expanded="True">
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
77 <param name="sigma" type="integer" value="6" label="Multiplier of the standard deviation" help="[sigma]" />
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
78 <param name="perfwhm" type="float" value="0.6" max="1" min="0" label="Percentage of FWHM width" help="[perfwhm]" />
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
79 </section>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
80
30
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
81 <section name="findgeneral" title="Annotation general options" expanded="True">
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
82 <param name="ppm" type="integer" value="5" label="General ppm error" help="[ppm]" />
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
83 <param name="mzabs" type="float" value="0.015" label="General absolut error in m/z" help="[mzabs]" />
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
84 </section>
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
85
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
86 <section name="findisotopes" title="Annotate Isotopes [findIsotopes]" expanded="True">
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
87 <param name="maxcharge" type="integer" value="3" label="Max. ion charge" help="[maxcharge]" />
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
88 <param name="maxiso" type="integer" value="4" label="Max. number of expected isotopes" help="[maxiso]" />
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
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]" />
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
90 </section>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
91
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
92 <conditional name="quick_block">
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
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">
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
94 <option value="FALSE" selected="true">All functions</option>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
95 <option value="TRUE">Only groupFWHM and findIsotopes functions [quick]</option>
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
96 </param>
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
97 <when value="FALSE">
30
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
98
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
99 <section name="groupcorr" title="Verifying grouping co-eluted peaks [groupCorr]" expanded="True">
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
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]" />
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
101 <param name="graphMethod" type="select" label="groupCorr: Method selection for grouping peaks after correlation analysis into pseudospectra" help="[graphMethod]">
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
102 <option value="hcs" selected="true">hcs</option>
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
103 <option value="lpc">lpc</option>
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
104 </param>
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
105 <param name="pval" type="float" value="0.05" max="1" min="0" label="groupCorr: significant correlation threshold" help="[pval]" />
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
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]"/>
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
107 <param name="calcIso" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use isotopic relationship for peak grouping" help="[calcIso]"/>
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
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]"/>
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
109 </section>
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
110
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
111 <section name="findadducts" title="Annotate Adducts [findAdducts]" expanded="True">
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
112 <param name="polarity" type="select" label="Which polarity mode was used for measuring of the ms sample" help="polarity">
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
113 <option value="positive" >positive</option>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
114 <option value="negative" selected="true">negative</option>
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
115 </param>
30
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
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]" />
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
117 <conditional name="rules_block">
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
118 <param name="rules_select" type="select" label="Use a personal ruleset file">
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
119 <option value="TRUE">TRUE</option>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
120 <option value="FALSE" selected="true">FALSE</option>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
121 </param>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
122 <when value="FALSE">
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
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]" />
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
124 </when>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
125 <when value="TRUE">
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
126 <param name="rules" type="data" format="csv" label="User defined ruleset" help="[rules]" />
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
127 </when>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
128 </conditional>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
129 </section>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
130
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
131 </when>
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
132 <when value="TRUE">
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
133 <param name="polarity" type="hidden" value="quick" label="for the output label" help="for the output label" />
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
134 </when>
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
135 </conditional>
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
136
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
137 <!-- Diffreport specific parameters -->
30
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
138 <section name="diffreport" title="Statistics and results export: [diffreport]" expanded="True">
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
139 <conditional name="options">
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
140 <param name="option" type="select" label="Number of condition">
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
141 <option value="hide" selected="true">One condition</option>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
142 <option value="show">Two or more conditions</option>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
143 </param>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
144 <when value="show">
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
145 <param name="eicmax" type="integer" value="0" label="Number of the most significantly different analytes to create EICs for" help="[eicmax]" />
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
146 <param name="eicwidth" type="integer" value="200" label="Width (in seconds) of EICs produced" help="[eicwidth]" />
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
147 <param name="value" type="select" label="Intensity values to be used for the diffreport" help="[value]">
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
148 <option value="into" selected="true">into</option>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
149 <option value="maxo" >maxo</option>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
150 <option value="intb">intb</option>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
151 </param>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
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]" />
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
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]" />
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
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]" />
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
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]"/>
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
156 <param name="tabular2" type="select" label="Export the Diffreport files in ">
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
157 <option value="zip" selected="true">Zip</option>
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
158 <option value="datasetcollection">Individual file in a Dataset Collection</option>
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
159 </param>
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
160 <param name="png2" type="select" label="Export the EIC and boxplots in ">
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
161 <option value="zip" selected="true">Zip</option>
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
162 <option value="pdf">Individual pdf</option>
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
163 </param>
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
164 </when>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
165 <when value="hide">
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
166 </when>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
167 </conditional>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
168 </section>
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
169
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
170 <expand macro="input_peaklist"/>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
171 <expand macro="input_file_load"/>
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
172 </inputs>
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
173
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
174 <outputs>
39
db9bc2c27a0a planemo upload commit d51a0d0a26833671b79711ee18d782e84f301e76
workflow4metabolomics
parents: 38
diff changeset
175 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
db9bc2c27a0a planemo upload commit d51a0d0a26833671b79711ee18d782e84f301e76
workflow4metabolomics
parents: 38
diff changeset
176 <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata" from_work_dir="annotatediff.RData">
32
23e33e354bb7 planemo upload commit 964980509aaa30c196b7ff20dbb78293f8286f06
lecorguille
parents: 30
diff changeset
177 <filter>quick_block['quick'] == 'FALSE'</filter>
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
178 <change_format>
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
179 <when input="quick_block.findadducts.polarity" value="positive" format="rdata.camera.positive" />
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
180 <when input="quick_block.findadducts.polarity" value="negative" format="rdata.camera.negative" />
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
181 </change_format>
1
a887bff50e45 Uploaded
lecorguille
parents: 0
diff changeset
182 </data>
39
db9bc2c27a0a planemo upload commit d51a0d0a26833671b79711ee18d782e84f301e76
workflow4metabolomics
parents: 38
diff changeset
183 <data name="rdata_quick_true" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.quick.Rdata" from_work_dir="annotatediff.RData">
32
23e33e354bb7 planemo upload commit 964980509aaa30c196b7ff20dbb78293f8286f06
lecorguille
parents: 30
diff changeset
184 <filter>quick_block['quick'] == 'TRUE'</filter>
30
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
185 </data>
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
186
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
187 <data name="output_diffreport_eic_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_eic.zip" from_work_dir="eic.zip" >
41
2350ab2c7e13 "planemo upload commit f978cc0a7aa81c244591e560f44970f0d61bf74e"
workflow4metabolomics
parents: 40
diff changeset
188 <filter>diffreport['options']['option'] == 'show' and diffreport['options']['eicmax'] > 0 and diffreport['options']['png2'] == 'zip'</filter>
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
189 </data>
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
190 <data name="output_diffreport_box_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_box.zip" from_work_dir="box.zip" >
41
2350ab2c7e13 "planemo upload commit f978cc0a7aa81c244591e560f44970f0d61bf74e"
workflow4metabolomics
parents: 40
diff changeset
191 <filter>diffreport['options']['option'] == 'show' and diffreport['options']['eicmax'] > 0 and diffreport['options']['png2'] == 'zip'</filter>
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
192 </data>
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
193 <collection name="output_diffreport_picture_pdf" type="list" label="${image.name[:-6]}.annotateDiffreport.pdf">
41
2350ab2c7e13 "planemo upload commit f978cc0a7aa81c244591e560f44970f0d61bf74e"
workflow4metabolomics
parents: 40
diff changeset
194 <filter>diffreport['options']['option'] == 'show' and diffreport['options']['eicmax'] > 0 and diffreport['options']['png2'] == 'pdf'</filter>
37
636e36a64d31 planemo upload commit a5f400649acb64e1c66a92379027ac5abdb4f546
lecorguille
parents: 36
diff changeset
195 <discover_datasets pattern="__designation_and_ext__" directory="pdf" format="pdf" />
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
196 </collection>
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
197
38
2184c0435edf planemo upload commit 1a6afbfa49a17d904e4e3cd01439f7ead41a0e33-dirty
lecorguille
parents: 37
diff changeset
198 <data name="output_diffreport_table_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_table.zip" from_work_dir="tabular.zip">
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
199 <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'zip'</filter>
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
200 </data>
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
201 <collection name="output_diffreport_table_collection" type="list" label="${image.name[:-6]}.annotateDiffreport_table">
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
202 <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'datasetcollection'</filter>
37
636e36a64d31 planemo upload commit a5f400649acb64e1c66a92379027ac5abdb4f546
lecorguille
parents: 36
diff changeset
203 <discover_datasets pattern="__designation_and_ext__" directory="tabular" format="tabular" />
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
204 </collection>
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
205 </outputs>
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
206 <tests>
45
db77f2b67a7f planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58
workflow4metabolomics
parents: 44
diff changeset
207 <test expect_num_outputs="5">
43
7f4ae4db39eb "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998"
workflow4metabolomics
parents: 42
diff changeset
208 <param name="image" value="faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.RData"/>
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
209 <expand macro="test_annotate_diffreport"/>
30
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
210 <expand macro="test_annotate_quick_true"/>
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
211 <expand macro="test_file_load_single"/>
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
212 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" lines_diff="2" />
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
213 </test>
45
db77f2b67a7f planemo upload commit cfad09eb4dd6b1439b7de6a0852cd8fa22210f58
workflow4metabolomics
parents: 44
diff changeset
214 <test expect_num_outputs="5">
43
7f4ae4db39eb "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998"
workflow4metabolomics
parents: 42
diff changeset
215 <param name="image" value="faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.RData"/>
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
216 <expand macro="test_annotate_diffreport"/>
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
217 <conditional name="quick_block">
30
fce12d692a41 planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents: 28
diff changeset
218 <expand macro="test_annotate_quick_false" />
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
219 <section name="findadducts">
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
220 <param name="polarity" value="negative"/>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
221 <conditional name="rules_block">
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
222 <param name="rules_select" value="TRUE"/>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
223 <param name="rules" value="CASMI_extended_NEG_rules.csv" ftype="csv"/>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
224 </conditional>
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
225 </section>
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
226 </conditional>
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
227 <expand macro="test_file_load_single"/>
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
228 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv" lines_diff="2"/>
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
229 </test>
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
230 </tests>
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
231
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
232
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
233
1
a887bff50e45 Uploaded
lecorguille
parents: 0
diff changeset
234 <help><![CDATA[
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
235
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 6
diff changeset
236 @HELP_AUTHORS@
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
237
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
238 ================
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
239 CAMERA.annotate
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
240 ================
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
241
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
242 -----------
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
243 Description
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
244 -----------
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
245
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
246 The R-package CAMERA is a Collection of Algorithms for MEtabolite
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
247 pRofile Annotation. Its primary purpose is the annotation and evaluation of
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
248 LC-MS data. It includes algorithms for annotation of isotope peaks, adducts
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
249 and fragments in peak lists. Additional methods cluster mass signals that
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
250 originate from a single metabolite, based on rules for mass differences and
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
251 peak shape comparison. To use the strength of already existing programs,
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
252 CAMERA is designed to interact directly with processed peak data from the
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
253 R-package **xcms**.
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
254
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
255 **What it does?**
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
256
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
257 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
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
258
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
259 If you have two or more conditions, it will return a diffreport result within the annotation results.
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
260 The diffreport result shows the most significant differences between two sets of samples. Optionally
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
261 create extracted ion chromatograms for the most significant differences.
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
262
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
263
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
264 -----------------
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
265 Workflow position
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
266 -----------------
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
267
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
268
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
269 **Upstream tools**
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
270
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
271 ========================= ==================== ====================== ==========
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
272 Name output file format parameter
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
273 ========================= ==================== ====================== ==========
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
274 xcms.fillPeaks xset.fillPeaks.RData rdata.xcms.fillpeaks RData file
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
275 ========================= ==================== ====================== ==========
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
276
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
277
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
278 **Downstream tools**
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
279
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
280 +---------------------------+---------------------------------------+------------------------------------------------+
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
281 | Name | Output file | Format |
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
282 +===========================+=======================================+================================================+
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
283 |CAMERA_combinexsAnnot |xset.annotate.Rdata | rdata.camera.positive or rdata.camera.negative |
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
284 +---------------------------+---------------------------------------+------------------------------------------------+
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
285 |Determine Vdk or Lowess |xset.annotate.variableMetadata.tsv | Tabular |
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
286 +---------------------------+---------------------------------------+------------------------------------------------+
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
287 |Normalization Vdk/Lowess |xset.annotate.variableMetadata.tsv | Tabular |
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
288 +---------------------------+---------------------------------------+------------------------------------------------+
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
289 |Anova |xset.annotate.variableMetadata.tsv | Tabular |
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
290 +---------------------------+---------------------------------------+------------------------------------------------+
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
291 |PCA |xset.annotate.variableMetadata.tsv | Tabular |
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
292 +---------------------------+---------------------------------------+------------------------------------------------+
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
293 |Hierarchical Clustering |xset.annotate.variableMetadata.tsv | Tabular |
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
294 +---------------------------+---------------------------------------+------------------------------------------------+
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
295
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
296
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
297 The output file **xset.annotate.variableMetadata.tsv** is an tabular file. You can continue your analysis using it in the following tools:
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
298
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
299 | Determine Vdk or Lowess
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
300 | Normalization Vdk/Lowess
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
301 | Anova
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
302 | PCA
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
303 | Hierarchical Clustering
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
304
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
305
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
306 **General schema of the metabolomic workflow**
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
307
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
308 .. image:: annotate_workflow.png
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
309
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
310 -----------
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
311 Input files
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
312 -----------
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
313
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
314 +---------------------------+---------------------------+
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
315 | Parameter : num + label | Format |
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
316 +===========================+===========================+
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
317 | 1 : RData file | rdata.xcms.fillpeaks |
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
318 +---------------------------+---------------------------+
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
319
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
320
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
321 [Optional] User defined ruleset:
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
322 --------------------------------
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
323
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
324 Example:
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
325
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
326 | "name","nmol","charge","massdiff","oidscore","quasi","ips"
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
327 | "[M-H]-",1,-1,-1.007276,1,1,1
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
328 | "[M-2H]2-",1,-2,-2.014552,2,0,1
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
329 | "[M-3H]3-",1,-3,-3.021828,3,0,1
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
330 | "[M-2H+Na]-",1,-1,20.974666,4,0,0.25
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
331 | "[M-H+Cl]2-",1,-2,33.962126,5,0,1
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
332 | "[M-2H+K]-",1,-1,36.948606,6,0,0.25
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
333 | "[M+Cl]-",1,-1,34.969402,7,1,1
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
334 | "[M+2Cl]2-",1,-2,69.938804,8,0,1
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
335 | "[2M-H]-",2,-1,-1.007276,1,0,0.5
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
336
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
337 ----------
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
338 Parameters
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
339 ----------
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
340
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
341 diffreport: Intensity values to be used for the diffreport
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
342 ----------------------------------------------------------
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
343
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
344 | If **value="into"**, integrated peak intensities are used.
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
345 | If **value="maxo"**, maximum peak intensities are used.
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
346 | If **value="intb"**, baseline corrected integrated peak intensities are used (only available if peak detection was done by ‘findPeaks.centWave’).
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
347
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
348
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
349
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
350 ------------
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
351 Output files
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
352 ------------
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
353
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
354 xset.annotate.variableMetadata.tsv
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
355
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
356 | For each metabolite (row) :
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
357 | the value of the intensity in each sample, fold, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct and pcgroup
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
358
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
359 xset.annotate.zip
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
360
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
361 | It contains filebase_eic, filebase_box and filebase.tsv for one conditon vs another (Anova analysis).
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
362
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
363 xset.annotate.Rdata rdata.camera.quick or rdata.camera.positive or rdata.camera.negative
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
364
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
365 | Rdata file, that be used outside Galaxy in R.
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
366
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
367 ------
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
368
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
369 .. class:: infomark
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
370
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
371 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
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
372
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
373 | Determine Vdk or Lowess (Data correction)
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
374 | Normalization Vdk/Lowess (Data correction)
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
375 | Anova (Statistical analysis)
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
376 | PCA (Statistical analysis)
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
377 | Hierarchical Clustering (Statistical analysis)
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
378
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
379
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
380 ---------------------------------------------------
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
381
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
382 ---------------
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
383 Working example
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
384 ---------------
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
385
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
386 Input files
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
387 -----------
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
388
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
389 | RData file -> **xset.fillPeaks.RData**
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
390
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
391 Parameters
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
392 ----------
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
393
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
394 | sortpval -> **false**
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
395 | sigma -> **6 (default)**
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
396 | perfwhm -> **0.6 (default)**
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
397 | maxcharge -> **3 (default)**
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
398 | maxiso -> **4 (default)**
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
399 | minfrac -> **0.5 (default)**
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
400 | ppm -> **500**
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
401 | mzabs -> **0.015(default)**
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
402 | Advanced options -> **hide**
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
403 | Numver of condition -> Two or more conditioons
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
404 | eicmax -> **200**
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
405 | eicwidth -> **200 (default)**
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
406
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
407
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
408
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
409 Output files
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
410 ------------
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
411
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
412 **Example of a part of xset.annotate.variableMetadata.tsv output**
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
413
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
414 .. image:: annotatediffreport_variableMetadata.png
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
415
6
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
416
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
417 ---------------------------------------------------
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
418
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
419 Changelog/News
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
420 --------------
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
421
37
636e36a64d31 planemo upload commit a5f400649acb64e1c66a92379027ac5abdb4f546
lecorguille
parents: 36
diff changeset
422 .. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS
636e36a64d31 planemo upload commit a5f400649acb64e1c66a92379027ac5abdb4f546
lecorguille
parents: 36
diff changeset
423
44
e7e7c9238467 "planemo upload commit 8c20c85850fa44e3ac0f560f2269e86a51b9ebf0"
workflow4metabolomics
parents: 43
diff changeset
424 @HELP_CAMERA_NEWVERSION_1480@
e7e7c9238467 "planemo upload commit 8c20c85850fa44e3ac0f560f2269e86a51b9ebf0"
workflow4metabolomics
parents: 43
diff changeset
425
43
7f4ae4db39eb "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998"
workflow4metabolomics
parents: 42
diff changeset
426 @HELP_CAMERA_NEWVERSION_1460@
7f4ae4db39eb "planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998"
workflow4metabolomics
parents: 42
diff changeset
427
42
2cb22478651f "planemo upload commit e363c270e2f9d72cb0ede1a7f3bc61418b72c4c4"
workflow4metabolomics
parents: 41
diff changeset
428 **Version 2.2.6+camera1.42.0-galaxy1 - 09/03/2020**
41
2350ab2c7e13 "planemo upload commit f978cc0a7aa81c244591e560f44970f0d61bf74e"
workflow4metabolomics
parents: 40
diff changeset
429
2350ab2c7e13 "planemo upload commit f978cc0a7aa81c244591e560f44970f0d61bf74e"
workflow4metabolomics
parents: 40
diff changeset
430 - BUGFIX: Fix the zip export of the pictures (eic and boxplot)
2350ab2c7e13 "planemo upload commit f978cc0a7aa81c244591e560f44970f0d61bf74e"
workflow4metabolomics
parents: 40
diff changeset
431
40
3d943f088143 "planemo upload commit 4fcbbcbc6d6b0a59e801870d31fe886a920ef429"
workflow4metabolomics
parents: 39
diff changeset
432 @HELP_CAMERA_NEWVERSION_1420@
3d943f088143 "planemo upload commit 4fcbbcbc6d6b0a59e801870d31fe886a920ef429"
workflow4metabolomics
parents: 39
diff changeset
433
37
636e36a64d31 planemo upload commit a5f400649acb64e1c66a92379027ac5abdb4f546
lecorguille
parents: 36
diff changeset
434 **Version 2.2.5 - 09/04/2019**
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
435
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
436 - NEW: zip export are back for pictures (eic and boxplot) and diffreport tables
39
db9bc2c27a0a planemo upload commit d51a0d0a26833671b79711ee18d782e84f301e76
workflow4metabolomics
parents: 38
diff changeset
437
37
636e36a64d31 planemo upload commit a5f400649acb64e1c66a92379027ac5abdb4f546
lecorguille
parents: 36
diff changeset
438 - UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_)
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
439
39
db9bc2c27a0a planemo upload commit d51a0d0a26833671b79711ee18d782e84f301e76
workflow4metabolomics
parents: 38
diff changeset
440 - UPGRADE: refactoring of internal code
db9bc2c27a0a planemo upload commit d51a0d0a26833671b79711ee18d782e84f301e76
workflow4metabolomics
parents: 38
diff changeset
441
36
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
442 **Version 2.2.4 - 09/10/2018**
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
443
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
444 - NEW: CAMERA.annotate no longer export a DataMatrix. fillChromPeaks does the job
b6a8143c397c planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00
lecorguille
parents: 35
diff changeset
445
35
b02797fbead1 planemo upload commit 688b63e161c4df4364d248bf78536a7649564db4
lecorguille
parents: 34
diff changeset
446 **Version 2.2.3 - 30/04/2018**
b02797fbead1 planemo upload commit 688b63e161c4df4364d248bf78536a7649564db4
lecorguille
parents: 34
diff changeset
447
b02797fbead1 planemo upload commit 688b63e161c4df4364d248bf78536a7649564db4
lecorguille
parents: 34
diff changeset
448 - NEW: support the new xcms 3.0.0 wrapper
b02797fbead1 planemo upload commit 688b63e161c4df4364d248bf78536a7649564db4
lecorguille
parents: 34
diff changeset
449
34
34d89b4ad869 planemo upload commit 757700163128641f447d6fd089f2649d60a82f15
lecorguille
parents: 33
diff changeset
450 **Version 2.2.2 - 01/03/2018**
34d89b4ad869 planemo upload commit 757700163128641f447d6fd089f2649d60a82f15
lecorguille
parents: 33
diff changeset
451
34d89b4ad869 planemo upload commit 757700163128641f447d6fd089f2649d60a82f15
lecorguille
parents: 33
diff changeset
452 - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0
34d89b4ad869 planemo upload commit 757700163128641f447d6fd089f2649d60a82f15
lecorguille
parents: 33
diff changeset
453
34d89b4ad869 planemo upload commit 757700163128641f447d6fd089f2649d60a82f15
lecorguille
parents: 33
diff changeset
454 **Version 2.2.1 - 29/11/2017**
34d89b4ad869 planemo upload commit 757700163128641f447d6fd089f2649d60a82f15
lecorguille
parents: 33
diff changeset
455
34d89b4ad869 planemo upload commit 757700163128641f447d6fd089f2649d60a82f15
lecorguille
parents: 33
diff changeset
456 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
34d89b4ad869 planemo upload commit 757700163128641f447d6fd089f2649d60a82f15
lecorguille
parents: 33
diff changeset
457
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
458 **Version 2.2.0 - 28/03/2017**
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
459
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
460 - BUGFIX: the diffreport ids didn't convert the rt in minute as the other export
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
461
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
462 - 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.
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
463
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
464 - IMPROVEMENT: add some sections within to separate the different parts of the process
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
465
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
466 - IMPROVEMENT: add the possibility to use defined ruleset
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
467
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
468 - IMPROVEMENT: add the possibility to set the MZ digit within the identifiants
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
469
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
470 - IMPROVEMENT: CAMERA.annotate is now compatible with merged individual data from xcms.xcmsSet
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
471
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
472
14
e98ca7f0dcbd planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents: 11
diff changeset
473 **Version 2.1.5 - 21/04/2016**
e98ca7f0dcbd planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents: 11
diff changeset
474
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
475 - UPGRADE: upgrade the CAMERA version from 1.22.0 to 1.26.0
14
e98ca7f0dcbd planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents: 11
diff changeset
476
e98ca7f0dcbd planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents: 11
diff changeset
477
e98ca7f0dcbd planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents: 11
diff changeset
478 **Version 2.1.4 - 18/04/2016**
e98ca7f0dcbd planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents: 11
diff changeset
479
e98ca7f0dcbd planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents: 11
diff changeset
480 - TEST: refactoring to pass planemo test using conda dependencies
e98ca7f0dcbd planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents: 11
diff changeset
481
e98ca7f0dcbd planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents: 11
diff changeset
482
e98ca7f0dcbd planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents: 11
diff changeset
483 **Version 2.1.3 - 10/02/2016**
6
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
484
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
485 - BUGFIX: better management of errors. Datasets remained green although the process failed
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
486
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
487 - BUGFIX: the conversion into minutes of the retention time was applied to the diffreport outputs (several conditions)
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
488
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
489 - 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.
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
490
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
491 - UPDATE: refactoring of internal management of inputs/outputs
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
492
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
493
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
494 **VERSION 2.1.0 - 09/10/2015**
6
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
495
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
496 - BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don't match with the metabolites))
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
497
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
498
28
591d26b9027e planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents: 25
diff changeset
499 **VERSION 2.1.0 - 07/06/2015**
6
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
500
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
501 - 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.
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
502
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
503 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
504
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
505 - UPDATE: merged with annotateDiffreport. Some parameters are dedicated to experiences with several conditions
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
506
32b0e4bc881f Uploaded
lecorguille
parents: 5
diff changeset
507
1
a887bff50e45 Uploaded
lecorguille
parents: 0
diff changeset
508 ]]></help>
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
509
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents: 6
diff changeset
510 <expand macro="citation" />
0
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
511
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
512
b495191430d5 planemo upload
lecorguille
parents:
diff changeset
513 </tool>