Mercurial > repos > lecorguille > xcms_plot_chromatogram
diff macros.xml @ 2:e6fdadaf039e draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
| author | lecorguille |
|---|---|
| date | Tue, 03 Apr 2018 11:37:40 -0400 |
| parents | fe1f0f16d9e6 |
| children | a4a1143a202a |
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--- a/macros.xml Thu Mar 08 05:52:12 2018 -0500 +++ b/macros.xml Tue Apr 03 11:37:40 2018 -0400 @@ -1,22 +1,13 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">3.0.0</token> - <xml name="requirements"> - <requirements> - <requirement type="package" version="@WRAPPER_VERSION@">bioconductor-xcms</requirement> - <requirement type="package" version="1.1_4">r-batch</requirement> - <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> - <requirement type="package" version="6.0">unzip</requirement> - <yield /> - </requirements> - </xml> <xml name="stdio"> <stdio> <exit_code range="1" level="fatal" /> </stdio> </xml> - <token name="@COMMAND_XCMS_SCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token> + <!-- COMMAND --> + <token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token> <token name="@COMMAND_LOG_EXIT@"> ; @@ -25,6 +16,7 @@ sh -c "exit \$return" </token> + <!-- INPUT_VALIDATORS --> <xml name="input_validator_range_integer"> <validator type="regex" message="The format is 'min,max'" >[0-9]+ *, *[0-9]+</validator> </xml> @@ -37,155 +29,24 @@ <validator type="regex" message="The format is '1,2,4,6'" >[0-9, ]+</validator> </xml> + <token name="@INPUT_IMAGE_LABEL@">RData file</token> <token name="@INPUT_IMAGE_HELP@">It contain a xcms3::XCMSnExp object (named xdata)</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_zip_sacuri"> - <section name="file_load_section"> - <conditional name="file_load_conditional"> - <param name="file_load_select" value="yes" /> - <param name="input" value="sacuri_dir_root.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 - 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" from_work_dir="variableMetadata.tsv" > - <filter>(peaklist['peaklistBool'])</filter> - </data> - <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" from_work_dir="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 + <!-- MISC --> + <token name="@HELP_AUTHORS_WRAPPERS@"> .. 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] +**Galaxy integration** ABiMS TEAM - SU/CNRS - Station biologique de Roscoff and Yann Guitton - LABERCA +Part of Workflow4Metabolomics.org [W4M] | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. ---------------------------------------------------- - - </token> - - <token name="@HELP_XCMS_MANUAL@"> - -For details and explanations for all the parameters and the workflow of xcms_ package, see its manual_ and this example_ - -.. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html -.. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf -.. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html - </token> - <token name="@HELP_PEAKLIST@"> - -Get a Peak List ---------------- - -If 'true', the module generates two additional files corresponding to the peak list: -- the variable metadata file (corresponding to information about extracted ions such as mass or retention time) -- the data matrix (corresponding to related intensities) - -**decimal places for [mass or retention time] values in identifiers** - - | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time. - | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively. - | Theses parameters do not affect decimal places in columns other than the identifier one. - -**Reported intensity values** - - | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter: - | - into: integrated area of original (raw) peak - | - maxo: maximum intensity of original (raw) peak - | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’) - - </token> - - <xml name="citation"> - <citations> - <citation type="doi">10.1021/ac051437y</citation> + <xml name="citation_w4m"> <citation type="doi">10.1093/bioinformatics/btu813</citation> - </citations> </xml> </macros>