Mercurial > repos > charles-bernard > data_manager_build_alfa_indexes
view data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.xml @ 0:016200d4e379 draft
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author | charles-bernard |
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date | Thu, 27 Oct 2016 05:15:05 -0400 |
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children | 4ada30780811 |
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<tool id="build_alfa_indexes" name="ALFA indexes" version="0.0.1" tool_type="manage_data"> <description>build ALFA indexes from automatically downloaded gtf annotation file</description> <command interpreter="python">data_manager_build_alfa_indexes.py -e "${reference_source['kingdom']}" "${reference_source['species_name']}" -o "${out_file}" $__root_dir__ </command> <inputs> <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> <option value="ensembl" selected="True">Ensembl Genomes Websites</option> </param> <when value="ensembl"> <param name="kingdom" type="select" label="Select the ensembl website where to fetch the genome"> <option value="vertebrates" selected="True">Ensembl (Vertebrates)</option> <option value="bacteria" selected="True">Ensembl Bacteria</option> <option value="fungi" selected="True">Ensembl Fungi</option> <option value="metazoa" selected="True">Ensembl Metazoa</option> <option value="plants" selected="True">Ensembl Plants</option> <option value="protists" selected="True">Ensembl Protists</option> </param> <param name="species_name" type="text" value="Homo sapiens" label="Complete Species_Name" optional="False"> <validator type="empty_field" message="Please, enter a species name."/> </param> </when> </conditional> </inputs> <outputs> <data name="out_file" format="data_manager_json"/> </outputs> </tool>