Mercurial > repos > lecorguille > xcms_merge

annotate xcms_merge.xml @ 3:62b66b39a268 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312
author lecorguille
date Thu, 02 Mar 2017 08:21:35 -0500
parents 9063eaae5112
children 945652915244
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
1 <tool id="xcms_merge" name="xcms.xcmsSet Merger" version="1.0.0">
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
2 <description>Merge xcms.xcmsSet xset in one to be used by group</description>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
3
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
4 <macros>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
5 <import>macros.xml</import>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
6 </macros>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
7
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
8 <expand macro="requirements_light"/>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
9 <expand macro="stdio"/>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
10
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
11 <command><![CDATA[
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
12 Rscript $script_file
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
13 ]]></command>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
14
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
15 <configfiles>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
16 <configfile name="script_file"><![CDATA[
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
17 suppressPackageStartupMessages(library(xcms, quietly=TRUE))
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
18
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
19 images=c(
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
20 "${"\",\"".join(map(str, $images))}"
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
21 )
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
22
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
23
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
24 cat("\tXSET MERGING...\n")
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
25
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
26 for(image in images) {
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
27 load(image)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
28 cat(sampleNamesList\$sampleNamesOrigin,"\n")
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
29 if (!exists("xset_merged")) {
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
30 xset_merged=xset
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
31 singlefile_merged=singlefile
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
32 listOFlistArguments_merged=listOFlistArguments
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
33 md5sumList_merged=md5sumList
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
34 sampleNamesList_merged=sampleNamesList
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
35 } else {
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
36 xset_merged=c(xset_merged,xset)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
37 singlefile_merged=c(singlefile_merged,singlefile)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
38 listOFlistArguments_merged=c(listOFlistArguments_merged,listOFlistArguments)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
39 md5sumList_merged\$origin=rbind(md5sumList_merged\$origin,md5sumList\$origin)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
40 sampleNamesList_merged\$sampleNamesOrigin=c(sampleNamesList_merged\$sampleNamesOrigin,sampleNamesList\$sampleNamesOrigin)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
41 sampleNamesList_merged\$sampleNamesMakeNames=c(sampleNamesList_merged\$sampleNamesMakeNames,sampleNamesList\$sampleNamesMakeNames)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
42 }
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
43 }
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
44 rm(image)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
45 xset=xset_merged; rm(xset_merged)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
46 singlefile=singlefile_merged; rm(singlefile_merged)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
47 listOFlistArguments=listOFlistArguments_merged; rm(listOFlistArguments_merged)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
48 md5sumList=md5sumList_merged; rm(md5sumList_merged)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
49 sampleNamesList=sampleNamesList_merged; rm(sampleNamesList_merged)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
50
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
51 #if str($sampleMetadata) != 'None':
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
52 cat("\tXSET PHENODATA SETTING...\n")
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
53 sampleMetadata=read.table("$sampleMetadata", h=F, sep=";", stringsAsFactors=F)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
54 if (ncol(sampleMetadata) < 2) sampleMetadata=read.table("$sampleMetadata", h=F, sep="\t", stringsAsFactors=F)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
55 if (ncol(sampleMetadata) < 2) sampleMetadata=read.table("$sampleMetadata", h=F, sep=",", stringsAsFactors=F)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
56 if (ncol(sampleMetadata) < 2) {
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
57 error_message="Your sampleMetadata file seems not well formatted. The column separators accepted are ; , and tabulation"
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
58 print(error_message)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
59 stop(error_message)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
60 }
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
61
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
62 sampclass(xset)=sampleMetadata\$V2[match(rownames(xset@phenoData),sampleMetadata\$V1)]
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
63 #end if
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
64
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
65
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
66
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
67 cat("\tXSET OBJECT INFO\n")
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
68
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
69 print(xset@phenoData)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
70 print(xset)
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
71
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
72 cat("\tSAVE RData\n")
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
73 save.image("$xsetRData")
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
74
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
75 ]]></configfile>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
76 </configfiles>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
77
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
78 <inputs>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
79 <param name="images" type="data" format="rdata.xcms.raw,rdata" label="xset RData / xcms.xcmsSet file" help="output file from another xcms.xcmsSet" multiple="true" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
80 <param name="sampleMetadata" label="Sample metadata file " format="tabular" type="data" optional="true" help="must contain at least one column with the sample id and one column with the sample class"/>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
81 </inputs>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
82
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
83 <outputs>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
84 <data name="xsetRData" format="rdata.xcms.raw" label="xset.merged.RData" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
85 </outputs>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
86
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
87 <tests>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
88 <test>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
89 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
90 <assert_stdout>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
91 <has_text text="object with 4 samples" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
92 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
93 <has_text text="Mass range: 200.1-600 m/z" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
94 <has_text text="Peaks: 9251 (about 2313 per sample)" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
95 <has_text text="Peak Groups: 0" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
96 <has_text text="Sample classes: ." />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
97 </assert_stdout>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
98 </test>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
99 <test>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
100 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
101 <param name="sampleMetadata" value="sampleMetadata.tab" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
102 <assert_stdout>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
103 <has_text text="ko15 KO" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
104 <has_text text="ko16 KO" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
105 <has_text text="wt15 WT" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
106 <has_text text="wt16 WT" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
107 <has_text text="object with 4 samples" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
108 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
109 <has_text text="Mass range: 200.1-600 m/z" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
110 <has_text text="Peaks: 9251 (about 2313 per sample)" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
111 <has_text text="Peak Groups: 0" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
112 <has_text text="Sample classes: KO, WT" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
113 </assert_stdout>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
114 </test>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
115 <test>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
116 <param name="images" value="MM8-xset.RData,MM14-xset.RData" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
117 <assert_stdout>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
118 <has_text text="object with 2 samples" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
119 <has_text text="Time range: 19.7-307.3 seconds (0.3-5.1 minutes)" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
120 <has_text text="Mass range: 117.0357-936.7059 m/z" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
121 <has_text text="Peaks: 236 (about 118 per sample)" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
122 <has_text text="Peak Groups: 0" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
123 <has_text text="Sample classes: ." />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
124 </assert_stdout>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
125 </test>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
126 </tests>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
127
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
128 <help><![CDATA[
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
129
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
130 @HELP_AUTHORS@
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
131
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
132 ===================
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
133 Xcms.xcmsSet Merger
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
134 ===================
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
135
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
136 -----------
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
137 Description
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
138 -----------
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
139
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
140 This tool will allow you to run one xcms.xcmsSet process per sample in parallel and then to merge all RData images in one.
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
141 The result is then suitable for xcms.group.
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
142
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
143 You can provide a sampleMetadata table to attribute phenotypic value to your samples.
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
144
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
145
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
146 -----------------
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
147 Workflow position
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
148 -----------------
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
149
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
150 **Upstream tools**
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
151
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
152 ========================= ================= =================== ==========
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
153 Name output file format parameter
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
154 ========================= ================= =================== ==========
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
155 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
156 ------------------------- ----------------- ------------------- ----------
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
157 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
158 ------------------------- ----------------- ------------------- ----------
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
159 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
160 ------------------------- ----------------- ------------------- ----------
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
161 ... ... ... ...
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
162 ========================= ================= =================== ==========
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
163
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
164
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
165 **Downstream tools**
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
166
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
167 +---------------------------+--------------------+-----------------+
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
168 | Name | Output file | Format |
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
169 +===========================+====================+=================+
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
170 |xcms.group | xset.RData | rdata.xcms.raw |
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
171 +---------------------------+--------------------+-----------------+
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
172
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
173
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
174 -----------
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
175 Input files
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
176 -----------
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
177
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
178 +---------------------------+-----------------------+
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
179 | Parameter : num + label | Format |
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
180 +===========================+=======================+
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
181 | 1 : RData file | rdata.xcms.raw |
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
182 +---------------------------+-----------------------+
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
183 | 2 : RData file | rdata.xcms.raw |
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
184 +---------------------------+-----------------------+
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
185 | N : RData file | rdata.xcms.raw |
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
186 +---------------------------+-----------------------+
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
187 | Optional : sampleMetadata | tsv or csv |
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
188 +---------------------------+-----------------------+
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
189
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
190 Example of a sampleMetadata:
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
191
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
192 +---------------------------+------------+
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
193 |HU_neg_028 | bio |
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
194 +---------------------------+------------+
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
195 |HU_neg_034 | bio |
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
196 +---------------------------+------------+
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
197 |Blanc04 | blank |
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
198 +---------------------------+------------+
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
199 |Blanc06 | blank |
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
200 +---------------------------+------------+
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
201 |Blanc09 | blank |
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
202 +---------------------------+------------+
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
203
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
204 ------------
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
205 Output files
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
206 ------------
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
207
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
208 xset.merged.RData: rdata.xcms.raw format
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
209
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
210 | Rdata file that is necessary in the next step of the workflow "xcms.group".
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
211
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
212 ---------------------------------------------------
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
213
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
214 Changelog/News
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
215 --------------
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
216
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
217 **Version 1.0.0 - 03/02/2017**
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
218
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
219 - NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
220
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
221 ]]></help>
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
222
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
223 <expand macro="citation" />
9063eaae5112 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents:
diff changeset
224 </tool>