Mercurial > repos > mmonsoor > camera_combinexsannos
diff macros.xml @ 8:198b035d4848 draft
planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
| author | lecorguille |
|---|---|
| date | Fri, 07 Apr 2017 07:42:38 -0400 |
| parents | c23aa0cbc550 |
| children | a3024f51082d |
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--- a/macros.xml Wed Feb 01 12:24:21 2017 -0500 +++ b/macros.xml Fri Apr 07 07:42:38 2017 -0400 @@ -2,12 +2,11 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="0.4_1">r-snow</requirement> + <requirement type="package" version="0.4_1">r-snow</requirement> <requirement type="package" version="1.26.0">bioconductor-camera</requirement> <requirement type="package" version="2.26.0">bioconductor-multtest</requirement> - <requirement type="package" version="1.1_4">r-batch</requirement> - <requirement type="package" version="1.6.27">libpng</requirement> - <requirement type="package" version="1.3.20">graphicsmagick</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> + <requirement type="package" version="1.3.23">graphicsmagick</requirement> </requirements> </xml> <xml name="stdio"> @@ -19,33 +18,137 @@ <token name="@COMMAND_CAMERA_SCRIPT@"> LANG=C Rscript $__tool_directory__/CAMERA.r </token> - - <!-- zipfile load for planemo test --> - <token name="@COMMAND_ZIPFILE_LOAD@"> - #if $zipfile_load_conditional.zipfile_load_select == "yes": - #if $zipfile_load_conditional.zip_file: - zipfile $zipfile_load_conditional.zip_file + + <!-- raw 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 + #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> + + <!-- peaklist export option management --> + <token name="@COMMAND_PEAKLIST@"> + convertRTMinute $export.convertRTMinute + numDigitsMZ $export.numDigitsMZ + numDigitsRT $export.numDigitsRT + intval $export.intval </token> - <xml name="zipfile_load"> - <conditional name="zipfile_load_conditional"> - <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." > - <option value="no" >no need</option> - <option value="yes" selected="peakgroups">yes</option> + + <xml name="input_peaklist"> + <section name="export" title="Export options"> + <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="General used intensity value" 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 value="no"> - </when> - <when value="yes"> - <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> - </when> + </section> + </xml> + + <xml name="test_peaklist"> + <section name="export"> + <param name="convertRTMinute" value="True"/> + <param name="numDigitsMZ" value="4" /> + <param name="numDigitsRT" value="1" /> + <param name="intval" value="into"/> + </section> + </xml> + + <!-- annotate_diffreport <test> commun part --> + <xml name="test_annotate_diffreport"> + <section name="groupfwhm"> + <param name="sigma" value="6"/> + <param name="perfwhm" value="0.6"/> + </section> + <section name="findisotopes"> + <param name="maxcharge" value="3"/> + <param name="maxiso" value="4"/> + <param name="minfrac" value="0.5"/> + </section> + <section name="findgeneral"> + <param name="ppm" value="5"/> + <param name="mzabs" value="0.015"/> + <param name="max_peaks" value="100"/> + </section> + <section name="diffreport"> + <conditional name="options"> + <param name="option" value="show"/> + <param name="eicmax" value="200"/> + <param name="eicwidth" value="200"/> + <param name="value" value="into"/> + <param name="h" value="480"/> + <param name="w" value="640"/> + <param name="mzdec" value="2"/> + <param name="sortpval" value="False"/> + </conditional> + </section> + <expand macro="test_peaklist"/> + </xml> + + <xml name="test_annotate_quick_false"> + <param name="quick" value="FALSE"/> + <section name="groupcorr"> + <param name="cor_eic_th" value="0.75"/> + <param name="graphMethod" value="hcs"/> + <param name="pval" value="0.05"/> + <param name="calcCiS" value="True"/> + <param name="calcIso" value="False"/> + <param name="calcCaS" value="False"/> + </section> + </xml> + + <xml name="test_annotate_quick_true"> + <conditional name="quick_block"> + <param name="quick" value="TRUE"/> </conditional> </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 +**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