Mercurial > repos > dfornika > chewbbaca_createschema
view chewbbaca_createschema.xml @ 2:fed8439686cb draft
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author | dfornika |
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date | Fri, 21 Feb 2020 01:14:47 +0000 |
parents | 470f58372a68 |
children | 75d3a1fb5f5a |
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<tool id="chewbbaca_createschema" name="chewBBACA CreateSchema" version="@TOOL_VERSION@+galaxy0"> <description>Adapt an external schema to be used with chewBBACA.</description> <requirements> <requirement type="package" version="@TOOL_VERSION@">chewbbaca</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ chewBBACA.py CreateSchema --cpu \${GALAXY_SLOTS:-1} -i '${assemblies}' #if str( prodigal_training_file_source.prodigal_training_file_source_selector ) == 'tool_data_table' --ptf '${prodigal_training_file_source.prodigal_training_file.fields.path}' #elif str( prodigal_training_file_source.prodigal_training_file_source_selector ) == 'history' --ptf '${prodigal_training_file_source.prodigal_training_file}' #end if #if str( cds ) != "": --CDS '${cds}' #end if --bsr '${bsr}' --len '${len}' -o schema && tar -czf schema.tgz schema ]]> </command> <inputs> <param name="assemblies" format="fasta" type="data" multiple="true" label="Assembled genomes (fasta)" /> <conditional name="prodigal_training_file_source"> <param name="prodigal_training_file_source_selector" type="select" label="Select a Prodigal training file from your history or use one from a tool data table?"> <option value="No" selected="true">No Prodigal training file</option> <option value="tool_data_table">Prodigal training file from tool data table</option> <option value="history">Prodigal training file from history</option> </param> <when value="No"/> <when value="tool_data_table"> <param name="prodigal_training_file" type="select" format="tabular" label="Prodigal Training File"> <options from_data_table="chewbbaca_prodigal_training_files"> <validator type="no_options" message="No chewBBACA prodigal training files are available" /> </options> </param> </when> <when value="history"> <param name="prodigal_training_file" type="data" format="binary" label="Prodigal training file" help=""/> </when> </conditional> <param name="bsr" type="float" value="0.6" optional="true" label="BSR score" /> <param name="cds" type="data" format="fasta" optional="true" label="Coding sequence file for schema creation (fasta)" /> </inputs> <outputs> <data name="schema_zipped" format="zip" label="${tool.name}: on ${on_string}: Schema (zipped)" from_work_dir="schema.tgz"/> </outputs> <tests> </tests> <help><![CDATA[ ]]> </help> <expand macro="citations"/> </tool>