Mercurial > repos > lecorguille > xcms_fillpeaks
diff macros_xcms.xml @ 13:91c71f3808f3 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
| author | lecorguille |
|---|---|
| date | Tue, 18 Sep 2018 16:13:36 -0400 |
| parents | |
| children | 34fe699200ce |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_xcms.xml Tue Sep 18 16:13:36 2018 -0400 @@ -0,0 +1,244 @@ +<?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> + + <!-- FILE_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 saying 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> + + <xml name="test_file_load_single_ko15"> + <section name="file_load_section"> + <conditional name="file_load_conditional"> + <param name="file_load_select" value="yes" /> + <param name="input" value="ko15.CDF" ftype="netcdf" /> + </conditional> + </section> + </xml> + + <!-- PEAKLIST --> + <token name="@COMMAND_PEAKLIST@"> + #if $peaklist.peaklistBool + convertRTMinute $peaklist.convertRTMinute + numDigitsMZ $peaklist.numDigitsMZ + numDigitsRT $peaklist.numDigitsRT + intval $peaklist.intval + naTOzero $peaklist.naTOzero + #end if + </token> + + <xml name="input_peaklist"> + <conditional name="peaklist"> + <param name="peaklistBool" type="boolean" label="Get a Peak List" /> + <when value="true"> + <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/> + <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" /> + <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" /> + <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below"> + <option value="into" selected="true">into</option> + <option value="maxo">maxo</option> + <option value="intb">intb</option> + </param> + <param name="naTOzero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Replace the remain NA by 0 in the dataMatrix" help="Rather mandatory for some downstream statistical steps"/> + </when> + <when value="false" /> + </conditional> + </xml> + + <xml name="output_peaklist" token_function=""> + <data name="variableMetadata" format="tabular" label="${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_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> + + <token name="@HELP_PEAKLIST_OUTPUT@"> +xset.variableMetadata.tsv : tabular format + + | Table containing information about ions; can be used as one input of **Quality_Metrics** or **Generic_filter** modules. + +xset.dataMatrix.tsv : tabular format + + | Table containing ions' intensities; can be used as one input of **Quality_Metrics** or **Generic_filter** modules. + </token> + + <!-- CENTWAVE --> + <token name="@COMMAND_CENTWAVE@"> + ppm $methods.ppm + peakwidth "c($methods.peakwidth)" + + ## Advanced + snthresh $methods.CentWaveAdv.snthresh + prefilter "c($methods.CentWaveAdv.prefilter)" + mzCenterFun $methods.CentWaveAdv.mzCenterFun + integrate $methods.CentWaveAdv.integrate + mzdiff $methods.CentWaveAdv.mzdiff + fitgauss $methods.CentWaveAdv.fitgauss + noise $methods.CentWaveAdv.noise + verboseColumns $methods.CentWaveAdv.verboseColumns + </token> + + <xml name="input_centwave"> + <param argument="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="for the initial ROI definition." /> + <param argument="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="with the expected approximate peak width in chromatographic space."> + <expand macro="input_validator_range_float"/> + </param> + </xml> + + <xml name="input_centwaveAdv"> + <param argument="snthresh" type="integer" value="10" label="Signal to Noise ratio cutoff" /> + <param argument="prefilter" type="text" value="3,100" label="Prefilter step for for the first analysis step (ROI detection)" help="Separate by coma k, I. Mass traces are only retained if they contain at least ‘k‘ peaks with intensity ‘>= I‘."> + <expand macro="input_validator_range_integer"/> + </param> + <param argument="mzCenterFun" type="select" label="Name of the function to calculate the m/z center of the chromatographic peak" > + <option value="wMean">intensity weighted mean of the peak's m/z values</option> + <option value="mean">mean of the peak's m/z values</option> + <option value="apex">use the m/z value at the peak apex</option> + <option value="wMeanApex3">ntensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option> + <option value="meanApex3">mean of the m/z value of the peak apex and the m/z values left and right of it</option> + </param> + <param argument="integrate" type="select" label="Integration method" > + <option value="1">peak limits are found through descent on the mexican hat filtered data (more robust, but less exact)</option> + <option value="2">peak limits based on real data (more accurate but prone to noise)</option> + </param> + <param argument="mzdiff" type="float" value="-0.001" label="Minimum difference in m/z for peaks with overlapping retention times" help="can be negative to allow overlap" /> + <param argument="fitgauss" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="fitgauss" help="whether or not a Gaussian should be fitted to each peak" /> + <param argument="noise" type="integer" value="0" label="Noise filter" help="allowing to set a minimum intensity required for centroids to be considered in the first analysis step (centroids with intensity lower than ‘noise’ are omitted from ROI detection)." /> + <param argument="verboseColumns" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="verbose Columns" help="whether additional peak meta data columns should be returned" /> + </xml> + + <token name="@COMMAND_CENTWAVEADVROI@"> + #if $sectionROI.roiList: + roiList '$sectionROI.roiList' + firstBaselineCheck $sectionROI.firstBaselineCheck + #if $sectionROI.roiScales != "": + roiScales "c($sectionROI.roiScales)" + #end if + #end if + </token> + + <xml name="input_centwaveAdvROI" token_optional="true"> + <param argument="roiList" type="data" format="tabular" optional="@OPTIONAL@" label="List of regions-of-interest (ROI) representing detected mass traces" help="If ROIs are submitted the first analysis step is omitted and chromatographic peak detection is performed on the submitted ROIs. Each ROI is expected to have the following elements specified: ‘scmin’ (start scan index), ‘scmax’ (end scan index), ‘mzmin’ (minimum m/z), ‘mzmax’ (maximum m/z), ‘length’ (number of scans), ‘intensity’ (summed intensity)." /> + <param argument="firstBaselineCheck" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Is continuous data within regions of interest is checked to be above the first baseline." /> + <param argument="roiScales" type="text" value="" optional="true" label="Numeric vector defining the scale for each region of interest in ‘roiList’" help="Length equal to ‘roiList’ - Should be used for the centWave-wavelets (format 0.9,1,0.2)"> + <expand macro="input_validator_range_float"/> + </param> + </xml> + + <!-- MISC --> + <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 + +@HELP_AUTHORS_WRAPPERS@ + +--------------------------------------------------- + + </token> + + <token name="@HELP_XCMS_MANUAL@"> + +For details and explanations concerning all the parameters and 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> + + <xml name="citation"> + <citations> + <citation type="doi">10.1021/ac051437y</citation> + <expand macro="citation_w4m"/> + </citations> + </xml> +</macros>