Mercurial > repos > lecorguille > xcms_merge
diff xcms_merge.xml @ 0:47f9b1fd5ce6 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
| author | lecorguille |
|---|---|
| date | Thu, 20 Apr 2017 05:41:32 -0400 |
| parents | |
| children | 3a5204f14fff |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xcms_merge.xml Thu Apr 20 05:41:32 2017 -0400 @@ -0,0 +1,225 @@ +<tool id="xcms_merge" name="xcms.xcmsSet Merger" version="1.0.0"> + <description>Merge xcms.xcmsSet xset in one to be used by group</description> + + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements_light"/> + <expand macro="stdio"/> + + <command><![CDATA[ + Rscript $script_file + ]]></command> + + <configfiles> + <configfile name="script_file"><![CDATA[ +suppressPackageStartupMessages(library(xcms, quietly=TRUE)) + +images=c( +"${"\",\"".join(map(str, $images))}" +) + + +cat("\tXSET MERGING...\n") + +for(image in images) { + load(image) + cat(sampleNamesList\$sampleNamesOrigin,"\n") + if (!exists("xset_merged")) { + xset_merged=xset + singlefile_merged=singlefile + listOFlistArguments_merged=listOFlistArguments + md5sumList_merged=md5sumList + sampleNamesList_merged=sampleNamesList + } else { + xset_merged=c(xset_merged,xset) + singlefile_merged=c(singlefile_merged,singlefile) + listOFlistArguments_merged=c(listOFlistArguments_merged,listOFlistArguments) + md5sumList_merged\$origin=rbind(md5sumList_merged\$origin,md5sumList\$origin) + sampleNamesList_merged\$sampleNamesOrigin=c(sampleNamesList_merged\$sampleNamesOrigin,sampleNamesList\$sampleNamesOrigin) + sampleNamesList_merged\$sampleNamesMakeNames=c(sampleNamesList_merged\$sampleNamesMakeNames,sampleNamesList\$sampleNamesMakeNames) + } +} +rm(image) +xset=xset_merged; rm(xset_merged) +singlefile=singlefile_merged; rm(singlefile_merged) +listOFlistArguments=listOFlistArguments_merged; rm(listOFlistArguments_merged) +md5sumList=md5sumList_merged; rm(md5sumList_merged) +sampleNamesList=sampleNamesList_merged; rm(sampleNamesList_merged) + +#if str($sampleMetadata) != 'None': + cat("\tXSET PHENODATA SETTING...\n") + sampleMetadata=read.table("$sampleMetadata", h=F, sep=";", stringsAsFactors=F) + if (ncol(sampleMetadata) < 2) sampleMetadata=read.table("$sampleMetadata", h=F, sep="\t", stringsAsFactors=F) + if (ncol(sampleMetadata) < 2) sampleMetadata=read.table("$sampleMetadata", h=F, sep=",", stringsAsFactors=F) + if (ncol(sampleMetadata) < 2) { + error_message="Your sampleMetadata file seems not well formatted. The column separators accepted are ; , and tabulation" + print(error_message) + stop(error_message) + } + + sampclass(xset)=sampleMetadata\$V2[match(rownames(xset@phenoData),sampleMetadata\$V1)] +#end if + + + +cat("\tXSET OBJECT INFO\n") + +print(xset@phenoData) +print(xset) + +cat("\tSAVE RData\n") +save.image("$xsetRData") + + ]]></configfile> + </configfiles> + + <inputs> + <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" /> + <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"/> + </inputs> + + <outputs> + <data name="xsetRData" format="rdata.xcms.raw" label="xset.merged.RData" /> + </outputs> + + <tests> + <test> + <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" /> + <assert_stdout> + <has_text text="object with 4 samples" /> + <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" /> + <has_text text="Mass range: 200.1-600 m/z" /> + <has_text text="Peaks: 9251 (about 2313 per sample)" /> + <has_text text="Peak Groups: 0" /> + <has_text text="Sample classes: ." /> + </assert_stdout> + </test> + <test> + <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" /> + <param name="sampleMetadata" value="sampleMetadata.tab" /> + <assert_stdout> + <has_text text="ko15 KO" /> + <has_text text="ko16 KO" /> + <has_text text="wt15 WT" /> + <has_text text="wt16 WT" /> + <has_text text="object with 4 samples" /> + <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" /> + <has_text text="Mass range: 200.1-600 m/z" /> + <has_text text="Peaks: 9251 (about 2313 per sample)" /> + <has_text text="Peak Groups: 0" /> + <has_text text="Sample classes: KO, WT" /> + </assert_stdout> + </test> + <test> + <param name="images" value="MM8-xset.RData,MM14-xset.RData" /> + <assert_stdout> + <has_text text="object with 2 samples" /> + <has_text text="Time range: 19.7-307.3 seconds (0.3-5.1 minutes)" /> + <has_text text="Mass range: 117.0357-936.7059 m/z" /> + <has_text text="Peaks: 236 (about 118 per sample)" /> + <has_text text="Peak Groups: 0" /> + <has_text text="Sample classes: ." /> + </assert_stdout> + </test> + </tests> + + <help><![CDATA[ + +@HELP_AUTHORS@ + +=================== +Xcms.xcmsSet Merger +=================== + +----------- +Description +----------- + +This tool will allow you to run one xcms.xcmsSet process per sample in parallel and then to merge all RData images in one. +The result is then suitable for xcms.group. + +You can provide a sampleMetadata table to attribute phenotypic value to your samples. + + +----------------- +Workflow position +----------------- + +**Upstream tools** + +========================= ================= =================== ========== +Name output file format parameter +========================= ================= =================== ========== +xcms.xcmsSet xset.RData rdata.xcms.raw RData file +------------------------- ----------------- ------------------- ---------- +xcms.xcmsSet xset.RData rdata.xcms.raw RData file +------------------------- ----------------- ------------------- ---------- +xcms.xcmsSet xset.RData rdata.xcms.raw RData file +------------------------- ----------------- ------------------- ---------- +... ... ... ... +========================= ================= =================== ========== + + +**Downstream tools** + ++---------------------------+--------------------+-----------------+ +| Name | Output file | Format | ++===========================+====================+=================+ +|xcms.group | xset.RData | rdata.xcms.raw | ++---------------------------+--------------------+-----------------+ + +.. image:: xcms_merge_workflow.png + +----------- +Input files +----------- + ++---------------------------+-----------------------+ +| Parameter : num + label | Format | ++===========================+=======================+ +| 1 : RData file | rdata.xcms.raw | ++---------------------------+-----------------------+ +| 2 : RData file | rdata.xcms.raw | ++---------------------------+-----------------------+ +| N : RData file | rdata.xcms.raw | ++---------------------------+-----------------------+ +| Optional : sampleMetadata | tsv or csv | ++---------------------------+-----------------------+ + +Example of a sampleMetadata: + ++---------------------------+------------+ +|HU_neg_028 | bio | ++---------------------------+------------+ +|HU_neg_034 | bio | ++---------------------------+------------+ +|Blanc04 | blank | ++---------------------------+------------+ +|Blanc06 | blank | ++---------------------------+------------+ +|Blanc09 | blank | ++---------------------------+------------+ + +------------ +Output files +------------ + +xset.merged.RData: rdata.xcms.raw format + + | Rdata file that is necessary in the next step of the workflow "xcms.group". + +--------------------------------------------------- + +Changelog/News +-------------- + +**Version 1.0.0 - 03/02/2017** + +- NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group + + ]]></help> + + <expand macro="citation" /> +</tool>