Mercurial > repos > lecorguille > camera_annotate
annotate abims_CAMERA_annotateDiffreport.xml @ 32:23e33e354bb7 draft
planemo upload commit 964980509aaa30c196b7ff20dbb78293f8286f06
author | lecorguille |
---|---|
date | Wed, 05 Apr 2017 07:36:44 -0400 |
parents | fce12d692a41 |
children | 3b2b642542f6 |
rev | line source |
---|---|
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
1 <tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.0"> |
0 | 2 |
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 | 11 |
1 | 12 <command><![CDATA[ |
9
c02d80efba80
planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
6
diff
changeset
|
13 @COMMAND_CAMERA_SCRIPT@ |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
14 xfunction annotatediff |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
15 image '$image' |
1 | 16 |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
17 nSlaves \${GALAXY_SLOTS:-1} |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
18 |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
19 ## output |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
20 variableMetadataOutput '$variableMetadata' |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
21 dataMatrixOutput '$datamatrix' |
1 | 22 |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
23 ## groupFWHM |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
24 sigma $groupfwhm.sigma |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
25 perfwhm $groupfwhm.perfwhm |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
26 |
30
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
27 ## findGeneral |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
28 ppm $findgeneral.ppm |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
29 mzabs $findgeneral.mzabs |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
30 |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
31 ## findIsotopes |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
32 maxcharge $findisotopes.maxcharge |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
33 maxiso $findisotopes.maxiso |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
34 minfrac $findisotopes.minfrac |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
35 |
0 | 36 quick $quick_block.quick |
30
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
37 #if $quick_block.quick == "FALSE": |
32
23e33e354bb7
planemo upload commit 964980509aaa30c196b7ff20dbb78293f8286f06
lecorguille
parents:
30
diff
changeset
|
38 xsetRdataOutput '$rdata_quick_false' |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
39 |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
40 ## groupcorr |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
41 cor_eic_th $quick_block.groupcorr.cor_eic_th |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
42 graphMethod $quick_block.groupcorr.graphMethod |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
43 pval $quick_block.groupcorr.pval |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
44 calcCiS $quick_block.groupcorr.calcCiS |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
45 calcIso $quick_block.groupcorr.calcIso |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
46 calcCaS $quick_block.groupcorr.calcCaS |
30
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
47 |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
48 ## findadducts |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
49 polarity $quick_block.findadducts.polarity |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
50 max_peaks $quick_block.findadducts.max_peaks |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
51 #if $quick_block.findadducts.rules_block.rules_select == "FALSE": |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
52 multiplier $quick_block.findadducts.rules_block.multiplier |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
53 #else |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
54 rules $quick_block.findadducts.rules_block.rules |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
55 #end if |
32
23e33e354bb7
planemo upload commit 964980509aaa30c196b7ff20dbb78293f8286f06
lecorguille
parents:
30
diff
changeset
|
56 #else |
23e33e354bb7
planemo upload commit 964980509aaa30c196b7ff20dbb78293f8286f06
lecorguille
parents:
30
diff
changeset
|
57 xsetRdataOutput '$rdata_quick_true' |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
58 #end if |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
59 |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
60 #if $diffreport.options.option == "show": |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
61 ## diffreport |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
62 runDiffreport TRUE |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
63 eicmax $diffreport.options.eicmax |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
64 eicwidth $diffreport.options.eicwidth |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
65 value $diffreport.options.value |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
66 sortpval $diffreport.options.sortpval |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
67 h $diffreport.options.h |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
68 w $diffreport.options.w |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
69 mzdec $diffreport.options.mzdec |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
70 new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_ |
0 | 71 #end if |
72 | |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
73 @COMMAND_PEAKLIST@ |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
74 |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
75 @COMMAND_FILE_LOAD@ |
11
d33e0ed5f32a
planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835-dirty
lecorguille
parents:
9
diff
changeset
|
76 |
1 | 77 ]]></command> |
0 | 78 |
79 <inputs> | |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
80 |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
81 |
0 | 82 <param name="image" type="data" label="RData file" format="rdata.xcms.fillpeaks,rdata" help="output file from another function xcms (fillPeaks)" /> |
83 | |
30
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
84 <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
|
85 <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
|
86 <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
|
87 </section> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
88 |
30
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
89 <section name="findgeneral" title="Annotation general options" expanded="True"> |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
90 <param name="ppm" type="integer" value="5" label="General ppm error" help="[ppm]" /> |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
91 <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
|
92 </section> |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
93 |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
94 <section name="findisotopes" title="Annotate Isotopes [findIsotopes]" expanded="True"> |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
95 <param name="maxcharge" type="integer" value="3" label="Max. ion charge" help="[maxcharge]" /> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
96 <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
|
97 <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
|
98 </section> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
99 |
0 | 100 <conditional name="quick_block"> |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
101 <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
|
102 <option value="FALSE" selected="true">All functions</option> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
103 <option value="TRUE">Only groupFWHM and findIsotopes functions [quick]</option> |
0 | 104 </param> |
105 <when value="FALSE"> | |
30
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
106 |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
107 <section name="groupcorr" title="Verifying grouping co-eluted peaks [groupCorr]" expanded="True"> |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
108 <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
|
109 <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
|
110 <option value="hcs" selected="true">hcs</option> |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
111 <option value="lpc">lpc</option> |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
112 </param> |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
113 <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
|
114 <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
|
115 <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
|
116 <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
|
117 </section> |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
118 |
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
119 <section name="findadducts" title="Annotate Adducts [findAdducts]" expanded="True"> |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
120 <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
|
121 <option value="positive" >positive</option> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
122 <option value="negative" selected="true">negative</option> |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
123 </param> |
30
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
124 <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
|
125 <conditional name="rules_block"> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
126 <param name="rules_select" type="select" label="Use a personal ruleset file"> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
127 <option value="TRUE">TRUE</option> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
128 <option value="FALSE" selected="true">FALSE</option> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
129 </param> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
130 <when value="FALSE"> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
131 <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
|
132 </when> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
133 <when value="TRUE"> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
134 <param name="rules" type="data" format="csv" label="User defined ruleset" help="[rules]" /> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
135 </when> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
136 </conditional> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
137 </section> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
138 |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
139 </when> |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
140 <when value="TRUE"> |
0 | 141 <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
|
142 </when> |
0 | 143 </conditional> |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
144 |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
145 <!-- Diffreport specific parameters --> |
30
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
146 <section name="diffreport" title="Statistics and results export: [diffreport]" expanded="True"> |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
147 <conditional name="options"> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
148 <param name="option" type="select" label="Number of condition"> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
149 <option value="hide" selected="true">One condition</option> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
150 <option value="show">Two or more conditions</option> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
151 </param> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
152 <when value="show"> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
153 <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
|
154 <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
|
155 <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
|
156 <option value="into" selected="true">into</option> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
157 <option value="maxo" >maxo</option> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
158 <option value="intb">intb</option> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
159 </param> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
160 <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
|
161 <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
|
162 <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
|
163 <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]"/> |
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 | 172 </inputs> |
173 | |
174 <outputs> | |
1 | 175 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" /> |
0 | 176 <data name="datamatrix" format="tabular" label="${image.name[:-6]}.annotate.dataMatrix.tsv" /> |
32
23e33e354bb7
planemo upload commit 964980509aaa30c196b7ff20dbb78293f8286f06
lecorguille
parents:
30
diff
changeset
|
177 <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata" > |
23e33e354bb7
planemo upload commit 964980509aaa30c196b7ff20dbb78293f8286f06
lecorguille
parents:
30
diff
changeset
|
178 <filter>quick_block['quick'] == 'FALSE'</filter> |
0 | 179 <change_format> |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
180 <when input="quick_block.findadducts.polarity" value="positive" format="rdata.camera.positive" /> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
181 <when input="quick_block.findadducts.polarity" value="negative" format="rdata.camera.negative" /> |
0 | 182 </change_format> |
1 | 183 </data> |
32
23e33e354bb7
planemo upload commit 964980509aaa30c196b7ff20dbb78293f8286f06
lecorguille
parents:
30
diff
changeset
|
184 <data name="rdata_quick_true" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.quick.Rdata" > |
23e33e354bb7
planemo upload commit 964980509aaa30c196b7ff20dbb78293f8286f06
lecorguille
parents:
30
diff
changeset
|
185 <filter>quick_block['quick'] == 'TRUE'</filter> |
30
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
186 </data> |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
187 <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="true"> |
32
23e33e354bb7
planemo upload commit 964980509aaa30c196b7ff20dbb78293f8286f06
lecorguille
parents:
30
diff
changeset
|
188 <filter>diffreport['options']['option'] == 'show'</filter> |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
189 </data> |
0 | 190 </outputs> |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
191 |
0 | 192 <tests> |
14
e98ca7f0dcbd
planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents:
11
diff
changeset
|
193 <test> |
e98ca7f0dcbd
planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents:
11
diff
changeset
|
194 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData"/> |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
195 <expand macro="test_annotate_diffreport"/> |
30
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
196 <expand macro="test_annotate_quick_true"/> |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
197 <expand macro="test_file_load_zip"/> |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
198 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" /> |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
199 <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" /> |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
200 </test> |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
201 <test> |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
202 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/> |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
203 <expand macro="test_annotate_diffreport"/> |
30
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
204 <expand macro="test_annotate_quick_true"/> |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
205 <expand macro="test_file_load_single"/> |
14
e98ca7f0dcbd
planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents:
11
diff
changeset
|
206 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" /> |
e98ca7f0dcbd
planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents:
11
diff
changeset
|
207 <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" /> |
0 | 208 </test> |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
209 <test> |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
210 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/> |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
211 <expand macro="test_annotate_diffreport"/> |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
212 <conditional name="quick_block"> |
30
fce12d692a41
planemo upload commit 2e3fcb07e9ff59974eaec8f868a9e78a63a89219
lecorguille
parents:
28
diff
changeset
|
213 <expand macro="test_annotate_quick_false" /> |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
214 <section name="findadducts"> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
215 <param name="polarity" value="negative"/> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
216 <conditional name="rules_block"> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
217 <param name="rules_select" value="TRUE"/> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
218 <param name="rules" value="CASMI_extended_NEG_rules.csv" ftype="csv"/> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
219 </conditional> |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
220 </section> |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
221 </conditional> |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
222 <expand macro="test_file_load_single"/> |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
223 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv" /> |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
224 <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.dataMatrix.tsv" /> |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
225 </test> |
0 | 226 </tests> |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
227 |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
228 |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
229 |
1 | 230 <help><![CDATA[ |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
231 |
9
c02d80efba80
planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
6
diff
changeset
|
232 @HELP_AUTHORS@ |
0 | 233 |
234 ================ | |
235 CAMERA.annotate | |
236 ================ | |
237 | |
238 ----------- | |
239 Description | |
240 ----------- | |
241 | |
242 The R-package CAMERA is a Collection of Algorithms for MEtabolite | |
243 pRofile Annotation. Its primary purpose is the annotation and evaluation of | |
244 LC-MS data. It includes algorithms for annotation of isotope peaks, adducts | |
245 and fragments in peak lists. Additional methods cluster mass signals that | |
246 originate from a single metabolite, based on rules for mass differences and | |
247 peak shape comparison. To use the strength of already existing programs, | |
248 CAMERA is designed to interact directly with processed peak data from the | |
249 R-package **xcms**. | |
250 | |
251 **What it does?** | |
252 | |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
253 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 | 254 |
255 If you have two or more conditions, it will return a diffreport result within the annotation results. | |
256 The diffreport result shows the most significant differences between two sets of samples. Optionally | |
257 create extracted ion chromatograms for the most significant differences. | |
258 | |
259 | |
260 ----------------- | |
261 Workflow position | |
262 ----------------- | |
263 | |
264 | |
265 **Upstream tools** | |
266 | |
267 ========================= ==================== ====================== ========== | |
268 Name output file format parameter | |
269 ========================= ==================== ====================== ========== | |
270 xcms.fillPeaks xset.fillPeaks.RData rdata.xcms.fillpeaks RData file | |
271 ========================= ==================== ====================== ========== | |
272 | |
273 | |
274 **Downstream tools** | |
275 | |
276 +---------------------------+---------------------------------------+------------------------------------------------+ | |
277 | Name | Output file | Format | | |
278 +===========================+=======================================+================================================+ | |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
279 |CAMERA_combinexsAnnot |xset.annotate.Rdata | rdata.camera.positive or rdata.camera.negative | |
0 | 280 +---------------------------+---------------------------------------+------------------------------------------------+ |
281 |Determine Vdk or Lowess |xset.annotate.dataMatrix.tsv | Tabular | | |
282 +---------------------------+---------------------------------------+------------------------------------------------+ | |
283 |Normalization Vdk/Lowess |xset.annotate.dataMatrix.tsv | Tabular | | |
284 +---------------------------+---------------------------------------+------------------------------------------------+ | |
285 |Anova |xset.annotate.dataMatrix.tsv | Tabular | | |
286 +---------------------------+---------------------------------------+------------------------------------------------+ | |
287 |PCA |xset.annotate.dataMatrix.tsv | Tabular | | |
288 +---------------------------+---------------------------------------+------------------------------------------------+ | |
289 |Hierarchical Clustering |xset.annotate.dataMatrix.tsv | Tabular | | |
290 +---------------------------+---------------------------------------+------------------------------------------------+ | |
291 | |
292 | |
293 The output file **xset.annotate.dataMatrix.tsv** is an tabular file. You can continue your analysis using it in the following tools: | |
294 | |
295 | Determine Vdk or Lowess | |
296 | Normalization Vdk/Lowess | |
297 | Anova | |
298 | PCA | |
299 | Hierarchical Clustering | |
300 | |
301 | |
302 **General schema of the metabolomic workflow** | |
303 | |
304 .. image:: annotate_workflow.png | |
305 | |
306 ----------- | |
307 Input files | |
308 ----------- | |
309 | |
310 +---------------------------+---------------------------+ | |
311 | Parameter : num + label | Format | | |
312 +===========================+===========================+ | |
313 | 1 : RData file | rdata.xcms.fillpeaks | | |
314 +---------------------------+---------------------------+ | |
315 | |
316 | |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
317 [Optional] User defined ruleset: |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
318 -------------------------------- |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
319 |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
320 Example: |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
321 |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
322 | "name","nmol","charge","massdiff","oidscore","quasi","ips" |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
323 | "[M-H]-",1,-1,-1.007276,1,1,1 |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
324 | "[M-2H]2-",1,-2,-2.014552,2,0,1 |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
325 | "[M-3H]3-",1,-3,-3.021828,3,0,1 |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
326 | "[M-2H+Na]-",1,-1,20.974666,4,0,0.25 |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
327 | "[M-H+Cl]2-",1,-2,33.962126,5,0,1 |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
328 | "[M-2H+K]-",1,-1,36.948606,6,0,0.25 |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
329 | "[M+Cl]-",1,-1,34.969402,7,1,1 |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
330 | "[M+2Cl]2-",1,-2,69.938804,8,0,1 |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
331 | "[2M-H]-",2,-1,-1.007276,1,0,0.5 |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
332 |
0 | 333 ---------- |
334 Parameters | |
335 ---------- | |
336 | |
337 diffreport: Intensity values to be used for the diffreport | |
338 ---------------------------------------------------------- | |
339 | |
340 | If **value="into"**, integrated peak intensities are used. | |
341 | If **value="maxo"**, maximum peak intensities are used. | |
342 | If **value="intb"**, baseline corrected integrated peak intensities are used (only available if peak detection was done by ‘findPeaks.centWave’). | |
343 | |
344 | |
345 | |
346 ------------ | |
347 Output files | |
348 ------------ | |
349 | |
350 xset.annotate.variableMetadata.tsv | |
351 | |
352 | For each metabolite (row) : | |
353 | the value of the intensity in each sample, fold, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct and pcgroup | |
354 | |
355 xset.annotate.dataMatrix.tsv | |
356 | |
357 | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column). | |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
358 |
0 | 359 xset.annotate.zip |
360 | |
361 | It contains filebase_eic, filebase_box and filebase.tsv for one conditon vs another (Anova analysis). | |
362 | |
363 xset.annotate.Rdata rdata.camera.quick or rdata.camera.positive or rdata.camera.negative | |
364 | |
365 | Rdata file, that be used outside Galaxy in R. | |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
366 |
0 | 367 ------ |
368 | |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
369 .. class:: infomark |
0 | 370 |
371 The output **"xset.annotate.dataMatrix.tsv"** is a tabular file. You can continue your analysis using it in the following tools of the workflow: | |
372 | |
373 | Determine Vdk or Lowess (Data correction) | |
374 | Normalization Vdk/Lowess (Data correction) | |
375 | Anova (Statistical analysis) | |
376 | PCA (Statistical analysis) | |
377 | Hierarchical Clustering (Statistical analysis) | |
378 | |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
379 |
0 | 380 --------------------------------------------------- |
381 | |
382 --------------- | |
383 Working example | |
384 --------------- | |
385 | |
386 Input files | |
387 ----------- | |
388 | |
389 | RData file -> **xset.fillPeaks.RData** | |
390 | |
391 Parameters | |
392 ---------- | |
393 | |
394 | sortpval -> **false** | |
395 | sigma -> **6 (default)** | |
396 | perfwhm -> **0.6 (default)** | |
397 | maxcharge -> **3 (default)** | |
398 | maxiso -> **4 (default)** | |
399 | minfrac -> **0.5 (default)** | |
400 | ppm -> **500** | |
401 | mzabs -> **0.015(default)** | |
402 | Advanced options -> **hide** | |
403 | Numver of condition -> Two or more conditioons | |
404 | eicmax -> **200** | |
405 | eicwidth -> **200 (default)** | |
406 | |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
407 |
0 | 408 |
409 Output files | |
410 ------------ | |
411 | |
412 **Example of an xset.annotate.dataMatrix.tsv output** | |
413 | |
414 .. image:: annotatediffreport_dataMatrix.png | |
415 | |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
416 **Example of a part of xset.annotate.variableMetadata.tsv output** |
0 | 417 |
418 .. image:: annotatediffreport_variableMetadata.png | |
419 | |
6 | 420 |
421 --------------------------------------------------- | |
422 | |
423 Changelog/News | |
424 -------------- | |
425 | |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
426 **Version 2.2.0 - 28/03/2017** |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
427 |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
428 - 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
|
429 |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
430 - 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
|
431 |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
432 - IMPROVEMENT: add some sections within to separate the different parts of the process |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
433 |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
434 - IMPROVEMENT: add the possibility to use defined ruleset |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
435 |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
436 - IMPROVEMENT: add the possibility to set the MZ digit within the identifiants |
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
437 |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
438 - IMPROVEMENT: CAMERA.annotate is now compatible with merged individual data from xcms.xcmsSet |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
439 |
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
440 |
14
e98ca7f0dcbd
planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents:
11
diff
changeset
|
441 **Version 2.1.5 - 21/04/2016** |
e98ca7f0dcbd
planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents:
11
diff
changeset
|
442 |
25
230f0bc9e792
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents:
23
diff
changeset
|
443 - 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
|
444 |
e98ca7f0dcbd
planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents:
11
diff
changeset
|
445 |
e98ca7f0dcbd
planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents:
11
diff
changeset
|
446 **Version 2.1.4 - 18/04/2016** |
e98ca7f0dcbd
planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents:
11
diff
changeset
|
447 |
e98ca7f0dcbd
planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents:
11
diff
changeset
|
448 - TEST: refactoring to pass planemo test using conda dependencies |
e98ca7f0dcbd
planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents:
11
diff
changeset
|
449 |
e98ca7f0dcbd
planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents:
11
diff
changeset
|
450 |
e98ca7f0dcbd
planemo upload commit 2761472c8afc41d54cecd54cabd1c5a5713514a3-dirty
lecorguille
parents:
11
diff
changeset
|
451 **Version 2.1.3 - 10/02/2016** |
6 | 452 |
453 - BUGFIX: better management of errors. Datasets remained green although the process failed | |
454 | |
455 - BUGFIX: the conversion into minutes of the retention time was applied to the diffreport outputs (several conditions) | |
456 | |
457 - 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. | |
458 | |
459 - UPDATE: refactoring of internal management of inputs/outputs | |
460 | |
461 | |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
462 **VERSION 2.1.0 - 09/10/2015** |
6 | 463 |
464 - BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don't match with the metabolites)) | |
465 | |
466 | |
28
591d26b9027e
planemo upload commit d708b85fc764e790fac071552d19cd7a89d02d31
lecorguille
parents:
25
diff
changeset
|
467 **VERSION 2.1.0 - 07/06/2015** |
6 | 468 |
469 - 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. | |
470 | |
471 - IMPROVEMENT: parameter labels have changed to facilitate their reading. | |
472 | |
473 - UPDATE: merged with annotateDiffreport. Some parameters are dedicated to experiences with several conditions | |
474 | |
475 | |
1 | 476 ]]></help> |
0 | 477 |
9
c02d80efba80
planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
6
diff
changeset
|
478 <expand macro="citation" /> |
0 | 479 |
480 | |
481 </tool> |