Mercurial > repos > lecorguille > xcms_merge
diff xcms_merge.xml @ 3:f439ed7a8f03 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
| author | lecorguille |
|---|---|
| date | Tue, 18 Sep 2018 16:09:25 -0400 |
| parents | 3a5204f14fff |
| children | a26679f68d4d |
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--- a/xcms_merge.xml Tue Feb 13 04:48:41 2018 -0500 +++ b/xcms_merge.xml Tue Sep 18 16:09:25 2018 -0400 @@ -1,99 +1,45 @@ -<tool id="xcms_merge" name="xcms.xcmsSet Merger" version="1.1.0"> - <description>Merge xcms.xcmsSet xset in one to be used by group</description> +<tool id="xcms_merge" name="xcms findChromPeaks Merger" version="@WRAPPER_VERSION@.0"> + <description>Merge xcms findChromPeaks RData into a unique file to be used by group</description> <macros> <import>macros.xml</import> + <import>macros_xcms.xml</import> </macros> - <expand macro="requirements_light"/> + <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ - Rscript $script_file + @COMMAND_RSCRIPT@/xcms_merge.r + + images 'c("${"\",\"".join(map(str, $images))}")' + + #if str($sampleMetadata) != 'None': + sampleMetadata '$sampleMetadata' + #end if + + @COMMAND_FILE_LOAD@ ]]></command> - <configfiles> - <configfile name="script_file"><![CDATA[ -suppressPackageStartupMessages(library(xcms, quietly=TRUE)) - -images=c( -"${"\",\"".join(map(str, $images))}" -) - - -cat("\tXSET MERGING...\n") - -for(image in images) { - load(image) - cat(sampleNamesList\$sampleNamesOrigin,"\n") - if (!exists("xset_merged")) { - xset_merged=xset - singlefile_merged=singlefile - listOFlistArguments_merged=listOFlistArguments - md5sumList_merged=md5sumList - sampleNamesList_merged=sampleNamesList - } else { - xset_merged=c(xset_merged,xset) - singlefile_merged=c(singlefile_merged,singlefile) - listOFlistArguments_merged=c(listOFlistArguments_merged,listOFlistArguments) - md5sumList_merged\$origin=rbind(md5sumList_merged\$origin,md5sumList\$origin) - sampleNamesList_merged\$sampleNamesOrigin=c(sampleNamesList_merged\$sampleNamesOrigin,sampleNamesList\$sampleNamesOrigin) - sampleNamesList_merged\$sampleNamesMakeNames=c(sampleNamesList_merged\$sampleNamesMakeNames,sampleNamesList\$sampleNamesMakeNames) - } -} -rm(image) -xset=xset_merged; rm(xset_merged) -singlefile=singlefile_merged; rm(singlefile_merged) -listOFlistArguments=listOFlistArguments_merged; rm(listOFlistArguments_merged) -md5sumList=md5sumList_merged; rm(md5sumList_merged) -sampleNamesList=sampleNamesList_merged; rm(sampleNamesList_merged) + <inputs> + <param name="images" type="data" format="rdata.xcms.findchrompeaks,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from multiple findChromPeaks" multiple="true" /> + <param name="sampleMetadata" label="Sample metadata file " format="tabular" type="data" optional="true" help="must contain at least one column with the sample id and one column with the sample class"/> -#if str($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("$sampleMetadata", h=F, sep=",", stringsAsFactors=F) - if (ncol(sampleMetadata) < 2) { - error_message="Your sampleMetadata file seems not well formatted. The column separators accepted are ; , and tabulation" - print(error_message) - stop(error_message) - } - - sampclass(xset)=sampleMetadata\$V2[match(rownames(xset@phenoData),sampleMetadata\$V1)] - - if (any(is.na(sampclass(xset)))) { - sample_missing <- rownames(phenoData(xset))[is.na(sampclass(xset))] - error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" ")) - print(error_message) - stop(error_message) - } -#end if - - - -cat("\tXSET OBJECT INFO\n") - -print(xset@phenoData) -print(xset) - -cat("\tSAVE RData\n") -save.image("$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"/> + <expand macro="input_file_load"/> </inputs> <outputs> - <data name="xsetRData" format="rdata.xcms.raw" label="xset.merged.RData" /> + <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="xset.merged.RData" from_work_dir="merged.RData" /> + <data name="sampleMetadataOutput" format="tabular" label="xset.merged.sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv"> + <filter>not sampleMetadata</filter> + </data> </outputs> <tests> + <!-- DISABLE FOR TRAVIS <test> - <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" /> + <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" ftype="rdata"/> + <expand macro="test_file_load_single"/> <assert_stdout> <has_text text="object with 4 samples" /> <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" /> @@ -102,15 +48,18 @@ <has_text text="Peak Groups: 0" /> <has_text text="Sample classes: ." /> </assert_stdout> + <output name="sampleMetadataOutput" file="noclass.merged.sampleMetadata.tsv" /> </test> + --> <test> - <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" /> + <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" ftype="rdata"/> + <expand macro="test_file_load_single"/> <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_matching expression="ko15\s+KO" /> + <has_text_matching expression="ko16\s+KO" /> + <has_text_matching expression="wt15\s+WT" /> + <has_text_matching expression="wt16\s+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" /> @@ -119,43 +68,32 @@ <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> - <test expect_failure="True"> - <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" /> + <!--<test expect_failure="True"> + <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" ftype="rdata"/> <param name="sampleMetadata" value="sampleMetadata_missing.tab" /> <expand macro="test_file_load_single"/> <assert_stderr> <has_text text="Those samples are missing in your sampleMetadata: ko16" /> </assert_stderr> - </test> + </test>--> </tests> <help><![CDATA[ @HELP_AUTHORS@ -=================== -Xcms.xcmsSet Merger -=================== +========================== +xcms findChromPeaks 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. +This tool allows you to run one xcms findChromPeaks process per sample in parallel and then to merge all RData images into one. +The result is then suitable for xcms groupChromPeaks. -You can provide a sampleMetadata table to attribute phenotypic value to your samples. +You can provide a sampleMetadata table to attribute phenotypic values to your samples. ----------------- @@ -164,26 +102,28 @@ **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 -------------------------- ----------------- ------------------- ---------- -... ... ... ... -========================= ================= =================== ========== +========================= ===================== ============================== +Name Output file Format +========================= ===================== ============================== +xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks +------------------------- --------------------- ------------------------------ +xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks +------------------------- --------------------- ------------------------------ +xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks +------------------------- --------------------- ------------------------------ +... ... ... +------------------------- --------------------- ------------------------------ +Upload file [optional] sampleMetadata tabular +========================= ===================== ============================== **Downstream tools** -+---------------------------+--------------------+-----------------+ -| Name | Output file | Format | -+===========================+====================+=================+ -|xcms.group | xset.RData | rdata.xcms.raw | -+---------------------------+--------------------+-----------------+ +=========================== ==================== ============================ +Name Output file Format +=========================== ==================== ============================ +xcms.groupChromPeaks xset.merged.RData rdata.xcms.findchrompeaks +=========================== ==================== ============================ .. image:: xcms_merge_workflow.png @@ -191,50 +131,60 @@ 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 | -+---------------------------+-----------------------+ +=========================== ================================== +Parameter : num + label Format +=========================== ================================== +1 : RData file rdata.xcms.findchrompeaks +--------------------------- ---------------------------------- +2 : RData file rdata.xcms.findchrompeaks +--------------------------- ---------------------------------- +N : RData file rdata.xcms.findchrompeaks +--------------------------- ---------------------------------- +Optional : sampleMetadata tsv or csv +=========================== ================================== Example of a sampleMetadata: -+---------------------------+------------+ -|HU_neg_028 | bio | -+---------------------------+------------+ -|HU_neg_034 | bio | -+---------------------------+------------+ -|Blanc04 | blank | -+---------------------------+------------+ -|Blanc06 | blank | -+---------------------------+------------+ -|Blanc09 | blank | -+---------------------------+------------+ +=========================== ============ +Samples class +=========================== ============ +HU_neg_028 bio +--------------------------- ------------ +HU_neg_034 bio +--------------------------- ------------ +Blanc04 blank +--------------------------- ------------ +Blanc06 blank +--------------------------- ------------ +Blanc09 blank +=========================== ============ + ------------ Output files ------------ -xset.merged.RData: rdata.xcms.raw format +xset.merged.RData: rdata.xcms.findchrompeaks format - | Rdata file that is necessary in the next step of the workflow "xcms.group". + | Rdata file that is necessary in the next step of the workflow "xcms.groupChromPeaks". --------------------------------------------------- Changelog/News -------------- +**Version 3.0.0.0 - 08/03/2018** + +- UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlining codes and methods + +- IMPROVMENT: a new dedicated tool "xcms plot chromatogram" will allow you to get TIC and BPI of your raw data. + +- IMPROVMENT: the tool will now generate a sampleMetadata file if any was provided. It will be useful to add some further information for the normalization and statistics steps. + **Version 1.0.1 - 13/02/2017** - IMPROVMENT: the tool will now raise an error if a sample isn't describe in the sampleMetadata file - **Version 1.0.0 - 03/02/2017** - NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group