Mercurial > repos > lecorguille > xcms_retcor

annotate abims_xcms_retcor.xml @ 29:33c0ca93f3ee draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
author workflow4metabolomics
date Mon, 03 Feb 2025 14:47:30 +0000
parents 8242376d9f35
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
27
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
1 <tool id="abims_xcms_retcor" name="xcms adjustRtime (retcor)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
2
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
3 <description>Retention Time Correction</description>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
4
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
5 <macros>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
6 <import>macros.xml</import>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
7 <import>macros_xcms.xml</import>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
8 </macros>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
9
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
10 <expand macro="requirements"/>
29
33c0ca93f3ee planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 27
diff changeset
11 <required_files>
33c0ca93f3ee planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 27
diff changeset
12 <include path="xcms_retcor.r" />
33c0ca93f3ee planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 27
diff changeset
13 <include path="lib.r" />
33c0ca93f3ee planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 27
diff changeset
14 </required_files>
27
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
15 <expand macro="stdio"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
16
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
17 <command><![CDATA[
29
33c0ca93f3ee planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
workflow4metabolomics
parents: 27
diff changeset
18 @COMMAND_RSCRIPT@xcms_retcor.r
27
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
19 image '$image'
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
20
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
21 method $methods.method
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
22 #if $methods.method == "PeakGroups":
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
23 minFraction $methods.minFraction
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
24 extraPeaks $methods.extraPeaks
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
25 smooth $methods.smooth_cond.smooth
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
26 ## PeakGroupsSmoothLoess Advanced
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
27 span $methods.smooth_cond.PeakGroupsSmoothLoessAdv.span
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
28 family $methods.smooth_cond.PeakGroupsSmoothLoessAdv.family
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
29 #else
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
30 binSize $methods.binSize
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
31 ## Advanced
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
32 #if $methods.ObiwarpAdv.centerSample != "":
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
33 centerSample $methods.ObiwarpAdv.centerSample
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
34 #end if
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
35 response $methods.ObiwarpAdv.response
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
36 distFun $methods.ObiwarpAdv.distFunCond.distFun
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
37 gapInit $methods.ObiwarpAdv.distFunCond.gapInit
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
38 gapExtend $methods.ObiwarpAdv.distFunCond.gapExtend
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
39 factorDiag $methods.ObiwarpAdv.factorDiag
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
40 factorGap $methods.ObiwarpAdv.factorGap
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
41 localAlignment $methods.ObiwarpAdv.localAlignmentCond.localAlignment
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
42 initPenalty $methods.ObiwarpAdv.localAlignmentCond.initPenalty
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
43 #end if
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
44
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
45 @COMMAND_FILE_LOAD@
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
46
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
47 @COMMAND_LOG_EXIT@
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
48 ]]></command>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
49
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
50 <inputs>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
51 <param name="image" type="data" format="rdata.xcms.findchrompeaks,rdata.xcms.group,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
52 <conditional name="methods">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
53 <param name="method" type="select" label="Method to use for retention time correction" help="See the help section below" >
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
54 <option value="PeakGroups" selected="true">PeakGroups - retention time correction based on aligment of features (peak groups) present in most/all samples.</option>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
55 <option value="Obiwarp">Obiwarp - alignment based on the complete mz-rt data.</option>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
56 </param>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
57 <when value="PeakGroups">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
58 <param argument="minFraction" type="float" value="0.9" min="0" max="1" label="Minimum required fraction of samples in which peaks for the peak group were identified" help="(previously missing)"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
59 <param argument="extraPeaks" type="integer" value="1" label="Maximal number of additional peaks for all samples to be assigned to a peak group for retention time correction" help="For a data set with 6 samples, ‘extraPeaks = 1’ uses all peak groups with a total peak count lower or equal to ‘6 + 1’. The total peak count is the total number of peaks being assigned to a peak group and considers also multiple peaks within a sample being assigned to the group. (previously extra)" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
60 <conditional name="smooth_cond">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
61 <param argument="smooth" type="select" label="Smooth method" >
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
62 <option value="loess" selected="true">loess - non-linear alignment</option>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
63 <option value="linear">linear - linear alignment</option>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
64 </param>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
65 <when value="loess">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
66 <section name="PeakGroupsSmoothLoessAdv" title="Advanced Options" expanded="False">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
67 <param argument="span" type="float" value="0.2" label="Degree of smoothing for the loess fitting" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
68 <param argument="family" type="select" label="Family" help="if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
69 <option value="gaussian" selected="true">gaussian</option>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
70 <option value="symmetric">symmetric</option>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
71 </param>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
72 </section>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
73 </when>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
74 <when value="linear" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
75 </conditional>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
76 </when>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
77 <when value="Obiwarp">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
78 <param argument="binSize" type="float" value="1" label="Bin size (in mz dimension) to be used for the profile matrix generation" help="See ‘step’ parameter in ‘profile-matrix’ documentation for more details. (previously profStep)" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
79 <section name="ObiwarpAdv" title="Advanced Options" expanded="False">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
80 <param argument="centerSample" type="integer" value="" optional="true" label="Index of the center sample in the experiment" help="It defaults to ‘floor(median(1:length(fileNames(object))))’" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
81 <param argument="response" type="integer" value="1" label="Defining the responsiveness of warping" help="with ‘response = 0’ giving linear warping on start and end points and ‘response = 100’ warping using all bijective anchors." />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
82 <conditional name="distFunCond">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
83 <param argument="distFun" type="select" label="Distance function to be used">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
84 <option value="cor_opt" selected="true">cor_opt - calculate only 10% diagonal band of distance matrix; better runtime</option>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
85 <option value="cor">cor - Pearson's correlation</option>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
86 <option value="cov">cov - covariance</option>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
87 <option value="prd">prd - product</option>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
88 <option value="euc">euc - Euclidian distance</option>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
89 </param>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
90 <when value="cor_opt">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
91 <param argument="gapInit" type="float" value="0.3" label="Penalty for gap opening" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
92 <param argument="gapExtend" type="float" value="2.4" label="Penalty for gap enlargement" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
93 </when>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
94 <when value="cor">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
95 <param argument="gapInit" type="float" value="0.3" label="Penalty for gap opening" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
96 <param argument="gapExtend" type="float" value="2.4" label="Penalty for gap enlargement" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
97 </when>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
98 <when value="cov">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
99 <param argument="gapInit" type="float" value="0.0" label="Penalty for gap opening" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
100 <param argument="gapExtend" type="float" value="11.7" label="Penalty for gap enlargement" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
101 </when>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
102 <when value="prd">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
103 <param argument="gapInit" type="float" value="0.0" label="Penalty for gap opening" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
104 <param argument="gapExtend" type="float" value="7.8" label="Penalty for gap enlargement" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
105 </when>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
106 <when value="euc">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
107 <param argument="gapInit" type="float" value="0.9" label="Penalty for gap opening" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
108 <param argument="gapExtend" type="float" value="1.8" label="Penalty for gap enlargement" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
109 </when>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
110 </conditional>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
111 <param argument="factorDiag" type="float" value="2" label="Local weight applied to diagonal moves in the alignment" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
112 <param argument="factorGap" type="float" value="1" label="local weight for gap moves in the alignment" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
113 <conditional name="localAlignmentCond">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
114 <param argument="localAlignment" type="select" label="Whether a local alignment should be performed instead of the default global alignment">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
115 <option value="FALSE" selected="true">FALSE</option>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
116 <option value="TRUE">TRUE</option>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
117 </param>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
118 <when value="FALSE">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
119 <param argument="initPenalty" type="hidden" value="0" label="Penalty for initiating an alignment" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
120 </when>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
121 <when value="TRUE">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
122 <param argument="initPenalty" type="float" value="0" label="Penalty for initiating an alignment" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
123 </when>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
124 </conditional>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
125 </section>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
126 </when>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
127 </conditional>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
128
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
129 <expand macro="input_file_load"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
130
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
131 </inputs>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
132
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
133 <outputs>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
134 <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.adjustRtime.RData" from_work_dir="retcor.RData" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
135 <data name="rawVSadjustedPdf" format="pdf" label="${image.name[:-6]}_rawVSadjusted.adjustRtime.Rplots.pdf" from_work_dir="raw_vs_adjusted_rt.pdf" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
136 </outputs>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
137
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
138 <tests>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
139 <test>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
140 <param name="image" value="faahKO-single-class.xset.merged.group.RData" ftype="rdata"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
141 <conditional name="methods">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
142 <param name="method" value="PeakGroups"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
143 <param name="extraPeaks" value="1"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
144 <param name="minFraction" value="1"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
145 <conditional name="smooth_cond">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
146 <param name="smooth" value="loess"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
147 <section name="PeakGroupsSmoothLoessAdv">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
148 <param name="span" value="0.2"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
149 <param name="family" value="gaussian"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
150 </section>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
151 </conditional>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
152 </conditional>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
153 <expand macro="test_file_load_single"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
154 <assert_stdout>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
155 <has_text text="extraPeaks: 1" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
156 <has_text text="minFraction: 1" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
157 <has_text text="span: 0.2" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
158 <has_text text="object with 4 samples" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
159 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
160 <has_text text="Mass range: 200.1-600 m/z" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
161 <has_text text="Peaks: 9251 (about 2313 per sample)" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
162 <has_text text="Peak Groups: 0" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
163 <has_text text="Sample classes: KO, WT" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
164 </assert_stdout>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
165 </test>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
166 <!-- DISABLE FOR TRAVIS : Zip
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
167 <test>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
168 <param name="image" value="faahKO.xset.group.RData" ftype="rdata"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
169 <conditional name="methods">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
170 <param name="method" value="PeakGroups"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
171 <param name="extraPeaks" value="1"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
172 <param name="minFraction" value="1"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
173 <conditional name="smooth_cond">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
174 <param name="smooth" value="loess"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
175 <section name="PeakGroupsSmoothLoessAdv">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
176 <param name="span" value="0.2"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
177 <param name="family" value="gaussian"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
178 </section>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
179 </conditional>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
180 </conditional>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
181 <expand macro="test_file_load_zip"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
182 <assert_stdout>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
183 <has_text text="object with 4 samples" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
184 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
185 <has_text text="Mass range: 200.1-600 m/z" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
186 <has_text text="Peaks: 9251 (about 2313 per sample)" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
187 <has_text text="Peak Groups: 0" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
188 <has_text text="Sample classes: KO, WT" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
189 </assert_stdout>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
190 </test>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
191 -->
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
192 <!-- DISABLE FOR TRAVIS
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
193 Test to test the different methods parameters
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
194 <test>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
195 <param name="image" value="faahKO-single-class.xset.group.RData" ftype="rdata"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
196 <conditional name="methods">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
197 <param name="method" value="Obiwarp"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
198 <section name="ObiwarpAdv">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
199 <param name="centerSample" value="1"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
200 <param name="response" value="0"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
201 <conditional name="distFunCond">
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
202 <param name="distFun" value="cov"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
203 <param name="gapInit" value="0.1" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
204 </conditional>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
205 </section>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
206 </conditional>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
207 <expand macro="test_file_load_single"/>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
208 <assert_stdout>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
209 <has_text text="centerSample: 1" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
210 <has_text text="response: 0" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
211 <has_text text="distFun: cov" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
212 <has_text text="gapInit: 0.1" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
213 <has_text text="gapExtend: 11.7" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
214 </assert_stdout>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
215 </test>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
216 -->
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
217 </tests>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
218
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
219 <help><![CDATA[
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
220
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
221 @HELP_AUTHORS@
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
222
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
223 ================
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
224 xcms adjustRtime
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
225 ================
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
226
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
227 -----------
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
228 Description
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
229 -----------
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
230
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
231 After matching peaks into groups, xcms can use those groups to identify and correct
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
232 correlated drifts in retention time from run to run. The aligned peaks can then be
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
233 used for a second pass of peak grouping which will be more accurate than the first.
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
234 The whole process can be repeated in an iterative fashion. Not all peak groups will be helpful
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
235 for identifying retention time drifts. Some groups may be missing peaks from a large
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
236 fraction of samples and thus provide an incomplete picture of the drift at that time point.
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
237 Still others may contain multiple peaks from the same sample, which is a sign of impropper grouping.
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
238
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
239 .. class:: warningmark
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
240
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
241 **After an adjustRtime step, it is mandatory to do a groupChromPeaks step, otherwise the rest of the workflow will not work with the RData file. (the initial peak grouping becomes invalid and is
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
242 discarded)**
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
243
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
244
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
245
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
246 -----------------
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
247 Workflow position
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
248 -----------------
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
249
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
250
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
251 **Upstream tools**
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
252
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
253 ========================= ============================ ==============================
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
254 Name Output file Format
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
255 ========================= ============================ ==============================
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
256 xcms.findChromPeaks raw.xset.RData rdata.xcms.findchrompeaks
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
257 ------------------------- ---------------------------- ------------------------------
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
258 xcms.groupChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
259 ========================= ============================ ==============================
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
260
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
261
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
262 **Downstream tools**
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
263
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
264 =========================== ============================ ================
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
265 Name Output file Format
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
266 =========================== ============================ ================
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
267 xcms.groupChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
268 =========================== ============================ ================
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
269
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
270
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
271 **General schema of the metabolomic workflow**
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
272
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
273 .. image:: xcms_retcor_workflow.png
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
274
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
275 ---------------------------------------------------
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
276
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
277 ----------
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
278 Parameters
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
279 ----------
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
280
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
281 Method
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
282 ------
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
283
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
284 **PeakGroups**
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
285
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
286 | This method performs retention time adjustment based on the alignment of chromatographic peak groups present in all/most samples (hence corresponding to house keeping compounds). First the retention time deviation of these peak groups is described by fitting either a polynomial (‘smooth = "loess"’) or a linear ( ‘smooth = "linear"’) model to the data points. These models are subsequently used to adjust the retention time of each spectrum in each sample.
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
287 | See the PeakGroups_manual_
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
288
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
289 **Obiwarp**
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
290
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
291 | This method performs retention time adjustment using the Obiwarp method [Prince 2006]. It is based on the code at http://obi-warp.sourceforge.net but supports alignment of multiple samples by aligning each against a _center_ sample. The alignment is performed directly on the ‘profile-matrix’ and can hence be performed independently of the peak detection or peak grouping.
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
292 | See the Obiwarp_manual_
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
293
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
294 .. _PeakGroups_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-peakGroups.html#heading-2
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
295 .. _Obiwarp_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-obiwarp.html
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
296
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
297 WARNING: if a retention time ajustment have already been applied to your data.
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
298 The function applyAdjustedRtime will replace raw retention times with adjusted retention times and so alloww to cumulate the ajustments.
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
299
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
300 @HELP_XCMS_MANUAL@
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
301
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
302 ------------
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
303 Output files
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
304 ------------
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
305
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
306 xset.groupChromPeaks.adjustRtime.RData: rdata.xcms.retcor format
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
307
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
308 | Rdata file that will be necessary in the **xcms.groupChromPeaks** step of the workflow.
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
309
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
310
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
311 ---------------------------------------------------
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
312
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
313 Changelog/News
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
314 --------------
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
315
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
316 @HELP_XCMS_NEWVERSION_31200@
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
317
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
318 **Version 3.6.1+galaxy1 - 13/02/2020**
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
319
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
320 - NEW: if a retention time ajustment have already been applied to your data. The function applyAdjustedRtime will replace raw retention times with adjusted retention times and so alloww to cumulate the ajustments.
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
321
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
322 @HELP_XCMS_NEWVERSION_3610@
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
323
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
324 **Version 3.4.4.1 - 30/04/2019**
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
325
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
326 - BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms.
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
327
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
328 @HELP_XCMS_NEWVERSION_3440@
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
329
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
330 **Version 3.0.0.0 - 08/03/2018**
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
331
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
332 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed.
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
333
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
334 - NEW: a bunch of new options: Obiwarp.(centerSample, response, distFun, gapInit, gapExtend, factorDiag, factorGap, localAlignment, initPenalty)
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
335
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
336 - IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values.
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
337
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
338 - CHANGE: removing of the TIC and BPC plots. You can now use the dedicated tool "xcms plot chromatogram"
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
339
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
340
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
341 **Version 2.1.1 - 29/11/2017**
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
342
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
343 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
344
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
345
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
346 **Version 2.1.0 - 03/02/2017**
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
347
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
348 - IMPROVEMENT: xcms.retcor can deal with merged individual data
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
349
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
350
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
351 **Version 2.0.8 - 22/12/2016**
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
352
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
353 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
354
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
355
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
356 @HELP_XCMS_NEWVERSION_2090@
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
357
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
358
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
359 **Version 2.0.6 - 04/04/2016**
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
360
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
361 - TEST: refactoring to pass planemo test using conda dependencies
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
362
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
363
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
364 **Version 2.0.5 - 10/02/2016**
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
365
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
366 - BUGFIX: better management of errors. Datasets remained green although the process failed
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
367
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
368 - BUGFIX: some pdf remained empty even when the process succeed
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
369
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
370 - UPDATE: refactoring of internal management of inputs/outputs
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
371
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
372 - UPDATE: refactoring to feed the new report tool
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
373
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
374
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
375 **Version 2.0.2 - 02/06/2015**
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
376
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
377 - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
378
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
379 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
380
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
381
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
382 ]]></help>
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
383
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
384
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
385 <expand macro="citation" />
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
386
8242376d9f35 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit cc13a2654ccf6f9e55bc0120ea5518df3b045712
workflow4metabolomics
parents:
diff changeset
387 </tool>