Mercurial > repos > lecorguille > ipo
view macros.xml @ 0:ac5f2936575b draft
planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
author | lecorguille |
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date | Thu, 03 Aug 2017 06:00:00 -0400 |
parents | |
children | ae8de756dfcf |
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<?xml version="1.0"?> <macros> <xml name="requirements"> <requirements> <requirement type="package" version="0.4_1">r-snow</requirement> <requirement type="package" version="1.0.0">bioconductor-ipo</requirement> <requirement type="package" version="1.1_4">r-batch</requirement> </requirements> </xml> <xml name="stdio"> <stdio> <exit_code range="1" level="fatal" /> </stdio> </xml> <token name="@COMMAND_SCRIPT@"> LANG=C Rscript $__tool_directory__/ </token> <token name="@COMMAND_LOG_EXIT@"> ; return=\$?; mv log.txt $log; cat $log; sh -c "exit \$return" </token> <token name="@COMMAND_NSLAVES@"> nSlaves \${GALAXY_SLOTS:-1} </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="@HELP_AUTHORS@"> .. class:: infomark **Authors** Gunnar Libiseller, Michaela Dvorzak, Ulrike Kleb, Edgar Gander, Tobias Eisenberg, Frank Madeo, Steffen Neumann, Gert Trausinger, Frank Sinner, Thomas Pieber and Christoph Magnes .. 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">10.1186/s12859-015-0562-8</citation> <citation type="doi">10.1093/bioinformatics/btu813</citation> </citations> </xml> </macros>