| Next changeset 1:090cf284d9ff (2017-11-29) |
|
Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797 |
|
added:
macros.xml repository_dependencies.xml static/images/xcms_merge_workflow.png test-data/MM14-xset.RData test-data/MM8-xset.RData test-data/ko15-xset.RData test-data/ko16-xset.RData test-data/sampleMetadata.tab test-data/wt15-xset.RData test-data/wt16-xset.RData xcms_merge.xml |
| b |
| diff -r 000000000000 -r 47f9b1fd5ce6 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Apr 20 05:41:32 2017 -0400 |
| [ |
| @@ -0,0 +1,141 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.4_1">r-snow</requirement> + <requirement type="package" version="1.46.0">bioconductor-xcms</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> + </requirements> + </xml> + <xml name="requirements_light"> + <requirements> + <requirement type="package" version="1.46.0">bioconductor-xcms</requirement> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1" level="fatal" /> + </stdio> + </xml> + + <token name="@COMMAND_XCMS_SCRIPT@"> + LANG=C Rscript $__tool_directory__/xcms.r + </token> + + <token name="@COMMAND_LOG_EXIT@"> + ; + return=\$?; + mv log.txt '$log'; + cat '$log'; + sh -c "exit \$return" + </token> + + <!-- zipfile load for planemo test --> + + <token name="@COMMAND_FILE_LOAD@"> + #if $file_load_section.file_load_conditional.file_load_select == "yes": + #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"): + #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] ) + #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] ) + + singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName' + #else + zipfile '$file_load_section.file_load_conditional.input' + #end if + #end if + </token> + + <xml name="input_file_load"> + <section name="file_load_section" title="Resubmit your raw dataset or your zip file"> + <conditional name="file_load_conditional"> + <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." > + <option value="no" >no need</option> + <option value="yes" >yes</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." /> + </when> + </conditional> + </section> + </xml> + + <xml name="test_file_load_zip"> + <section name="file_load_section"> + <conditional name="file_load_conditional"> + <param name="file_load_select" value="yes" /> + <param name="input" value="faahKO_reduce.zip" ftype="zip" /> + </conditional> + </section> + </xml> + + <xml name="test_file_load_single"> + <section name="file_load_section"> + <conditional name="file_load_conditional"> + <param name="file_load_select" value="yes" /> + <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> + </conditional> + </section> + </xml> + + <token name="@COMMAND_PEAKLIST@"> + #if $peaklist.peaklistBool + variableMetadataOutput '$variableMetadata' + dataMatrixOutput '$dataMatrix' + convertRTMinute $peaklist.convertRTMinute + numDigitsMZ $peaklist.numDigitsMZ + numDigitsRT $peaklist.numDigitsRT + intval $peaklist.intval + #end if + </token> + + <xml name="input_peaklist"> + <conditional name="peaklist"> + <param name="peaklistBool" type="boolean" label="Get a Peak List" /> + <when value="true"> + <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/> + <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" /> + <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" /> + <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below"> + <option value="into" selected="true">into</option> + <option value="maxo">maxo</option> + <option value="intb">intb</option> + </param> + </when> + <when value="false" /> + </conditional> + </xml> + + <xml name="output_peaklist" token_function=""> + <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv"> + <filter>(peaklist['peaklistBool'])</filter> + </data> + <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" > + <filter>(peaklist['peaklistBool'])</filter> + </data> + </xml> + + <token name="@HELP_AUTHORS@"> +.. class:: infomark + +**Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu + +.. class:: infomark + +**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M] + + | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. + +--------------------------------------------------- + + </token> + + + <xml name="citation"> + <citations> + <citation type="doi">10.1021/ac051437y</citation> + <citation type="doi">10.1093/bioinformatics/btu813</citation> + </citations> + </xml> +</macros> |
| b |
| diff -r 000000000000 -r 47f9b1fd5ce6 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Thu Apr 20 05:41:32 2017 -0400 |
| b |
| @@ -0,0 +1,5 @@ +<?xml version="1.0"?> +<repositories> + <repository changeset_revision="7800ba9a4c1e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="d64562a4ebb3" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories> |
| b |
| diff -r 000000000000 -r 47f9b1fd5ce6 static/images/xcms_merge_workflow.png |
| b |
| Binary file static/images/xcms_merge_workflow.png has changed |
| b |
| diff -r 000000000000 -r 47f9b1fd5ce6 test-data/MM14-xset.RData |
| b |
| Binary file test-data/MM14-xset.RData has changed |
| b |
| diff -r 000000000000 -r 47f9b1fd5ce6 test-data/MM8-xset.RData |
| b |
| Binary file test-data/MM8-xset.RData has changed |
| b |
| diff -r 000000000000 -r 47f9b1fd5ce6 test-data/ko15-xset.RData |
| b |
| Binary file test-data/ko15-xset.RData has changed |
| b |
| diff -r 000000000000 -r 47f9b1fd5ce6 test-data/ko16-xset.RData |
| b |
| Binary file test-data/ko16-xset.RData has changed |
| b |
| diff -r 000000000000 -r 47f9b1fd5ce6 test-data/sampleMetadata.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampleMetadata.tab Thu Apr 20 05:41:32 2017 -0400 |
| b |
| @@ -0,0 +1,6 @@ +wt16 WT +ko16 KO +wt15 WT +ko15 KO +ko10 KO +foobar01 FOOBAR |
| b |
| diff -r 000000000000 -r 47f9b1fd5ce6 test-data/wt15-xset.RData |
| b |
| Binary file test-data/wt15-xset.RData has changed |
| b |
| diff -r 000000000000 -r 47f9b1fd5ce6 test-data/wt16-xset.RData |
| b |
| Binary file test-data/wt16-xset.RData has changed |
| b |
| diff -r 000000000000 -r 47f9b1fd5ce6 xcms_merge.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xcms_merge.xml Thu Apr 20 05:41:32 2017 -0400 |
| [ |
| b'@@ -0,0 +1,225 @@\n+<tool id="xcms_merge" name="xcms.xcmsSet Merger" version="1.0.0">\n+ <description>Merge xcms.xcmsSet xset in one to be used by group</description>\n+\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+\n+ <expand macro="requirements_light"/>\n+ <expand macro="stdio"/>\n+\n+ <command><![CDATA[\n+ Rscript $script_file\n+ ]]></command>\n+\n+ <configfiles>\n+ <configfile name="script_file"><![CDATA[\n+suppressPackageStartupMessages(library(xcms, quietly=TRUE))\n+\n+images=c(\n+"${"\\",\\"".join(map(str, $images))}"\n+)\n+\n+\n+cat("\\tXSET MERGING...\\n")\n+\n+for(image in images) {\n+ load(image)\n+ cat(sampleNamesList\\$sampleNamesOrigin,"\\n")\n+ if (!exists("xset_merged")) {\n+ xset_merged=xset\n+ singlefile_merged=singlefile\n+ listOFlistArguments_merged=listOFlistArguments\n+ md5sumList_merged=md5sumList\n+ sampleNamesList_merged=sampleNamesList\n+ } else {\n+ xset_merged=c(xset_merged,xset)\n+ singlefile_merged=c(singlefile_merged,singlefile)\n+ listOFlistArguments_merged=c(listOFlistArguments_merged,listOFlistArguments)\n+ md5sumList_merged\\$origin=rbind(md5sumList_merged\\$origin,md5sumList\\$origin)\n+ sampleNamesList_merged\\$sampleNamesOrigin=c(sampleNamesList_merged\\$sampleNamesOrigin,sampleNamesList\\$sampleNamesOrigin)\n+ sampleNamesList_merged\\$sampleNamesMakeNames=c(sampleNamesList_merged\\$sampleNamesMakeNames,sampleNamesList\\$sampleNamesMakeNames)\n+ }\n+}\n+rm(image)\n+xset=xset_merged; rm(xset_merged)\n+singlefile=singlefile_merged; rm(singlefile_merged)\n+listOFlistArguments=listOFlistArguments_merged; rm(listOFlistArguments_merged)\n+md5sumList=md5sumList_merged; rm(md5sumList_merged)\n+sampleNamesList=sampleNamesList_merged; rm(sampleNamesList_merged)\n+\n+#if str($sampleMetadata) != \'None\':\n+ cat("\\tXSET PHENODATA SETTING...\\n")\n+ sampleMetadata=read.table("$sampleMetadata", h=F, sep=";", stringsAsFactors=F)\n+ if (ncol(sampleMetadata) < 2) sampleMetadata=read.table("$sampleMetadata", h=F, sep="\\t", stringsAsFactors=F)\n+ if (ncol(sampleMetadata) < 2) sampleMetadata=read.table("$sampleMetadata", h=F, sep=",", stringsAsFactors=F)\n+ if (ncol(sampleMetadata) < 2) {\n+ error_message="Your sampleMetadata file seems not well formatted. The column separators accepted are ; , and tabulation"\n+ print(error_message)\n+ stop(error_message)\n+ }\n+\n+ sampclass(xset)=sampleMetadata\\$V2[match(rownames(xset@phenoData),sampleMetadata\\$V1)]\n+#end if\n+\n+\n+\n+cat("\\tXSET OBJECT INFO\\n")\n+\n+print(xset@phenoData)\n+print(xset)\n+\n+cat("\\tSAVE RData\\n")\n+save.image("$xsetRData")\n+\n+ ]]></configfile>\n+ </configfiles>\n+\n+ <inputs>\n+ <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" />\n+ <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"/>\n+ </inputs>\n+\n+ <outputs>\n+ <data name="xsetRData" format="rdata.xcms.raw" label="xset.merged.RData" />\n+ </outputs>\n+\n+ <tests>\n+ <test>\n+ <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />\n+ <assert_stdout>\n+ <has_text text="object with 4 samples" />\n+ <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />\n+ <has_text text="Mass range: 200.1-600 m/z" />\n+ <has_text text="Peaks: 9251 (about 2313 per sample)" />\n+ <has_text text="Peak Groups: 0" />\n+ <has_text text="Sample classes: ." />\n+ </assert_stdout>\n+ </test>\n+ <test>\n+ <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />\n+ <param name'..b' text="Sample classes: KO, WT" />\n+ </assert_stdout>\n+ </test>\n+ <test>\n+ <param name="images" value="MM8-xset.RData,MM14-xset.RData" />\n+ <assert_stdout>\n+ <has_text text="object with 2 samples" />\n+ <has_text text="Time range: 19.7-307.3 seconds (0.3-5.1 minutes)" />\n+ <has_text text="Mass range: 117.0357-936.7059 m/z" />\n+ <has_text text="Peaks: 236 (about 118 per sample)" />\n+ <has_text text="Peak Groups: 0" />\n+ <has_text text="Sample classes: ." />\n+ </assert_stdout>\n+ </test>\n+ </tests>\n+\n+ <help><![CDATA[\n+\n+@HELP_AUTHORS@\n+\n+===================\n+Xcms.xcmsSet Merger\n+===================\n+\n+-----------\n+Description\n+-----------\n+\n+This tool will allow you to run one xcms.xcmsSet process per sample in parallel and then to merge all RData images in one.\n+The result is then suitable for xcms.group.\n+\n+You can provide a sampleMetadata table to attribute phenotypic value to your samples.\n+\n+\n+-----------------\n+Workflow position\n+-----------------\n+\n+**Upstream tools**\n+\n+========================= ================= =================== ==========\n+Name output file format parameter\n+========================= ================= =================== ==========\n+xcms.xcmsSet xset.RData rdata.xcms.raw RData file\n+------------------------- ----------------- ------------------- ----------\n+xcms.xcmsSet xset.RData rdata.xcms.raw RData file\n+------------------------- ----------------- ------------------- ----------\n+xcms.xcmsSet xset.RData rdata.xcms.raw RData file\n+------------------------- ----------------- ------------------- ----------\n+... ... ... ...\n+========================= ================= =================== ==========\n+\n+\n+**Downstream tools**\n+\n++---------------------------+--------------------+-----------------+\n+| Name | Output file | Format |\n++===========================+====================+=================+\n+|xcms.group | xset.RData | rdata.xcms.raw |\n++---------------------------+--------------------+-----------------+\n+\n+.. image:: xcms_merge_workflow.png\n+\n+-----------\n+Input files\n+-----------\n+\n++---------------------------+-----------------------+\n+| Parameter : num + label | Format |\n++===========================+=======================+\n+| 1 : RData file | rdata.xcms.raw |\n++---------------------------+-----------------------+\n+| 2 : RData file | rdata.xcms.raw |\n++---------------------------+-----------------------+\n+| N : RData file | rdata.xcms.raw |\n++---------------------------+-----------------------+\n+| Optional : sampleMetadata | tsv or csv |\n++---------------------------+-----------------------+\n+\n+Example of a sampleMetadata:\n+\n++---------------------------+------------+\n+|HU_neg_028 | bio |\n++---------------------------+------------+\n+|HU_neg_034 | bio |\n++---------------------------+------------+\n+|Blanc04 | blank |\n++---------------------------+------------+\n+|Blanc06 | blank |\n++---------------------------+------------+\n+|Blanc09 | blank |\n++---------------------------+------------+\n+\n+------------\n+Output files\n+------------\n+\n+xset.merged.RData: rdata.xcms.raw format\n+\n+ | Rdata file that is necessary in the next step of the workflow "xcms.group".\n+\n+---------------------------------------------------\n+\n+Changelog/News\n+--------------\n+\n+**Version 1.0.0 - 03/02/2017**\n+\n+- NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group\n+\n+ ]]></help>\n+\n+ <expand macro="citation" />\n+</tool>\n' |
