Mercurial > repos > devteam > data_manager_bwa_index_builder
view data_manager/bwa_color_space_index_builder.xml @ 0:367878cb3698 draft
Uploaded data manager definition.
author | devteam |
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date | Fri, 28 Mar 2014 14:18:43 -0400 |
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<tool id="bwa_color_space_index_builder_data_manager" name="BWA Color index" tool_type="manage_data" version="0.0.1"> <description>builder</description> <requirements> <requirement type="package" version="0.5.9">bwa</requirement> </requirements> <command interpreter="python">bwa_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" --data_table_name "bwa_indexes_color" --color_space</command> <inputs> <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> <options from_data_table="all_fasta"/> </param> <param type="text" name="sequence_name" value="" label="Name of sequence" /> <param type="text" name="sequence_id" value="" label="ID for sequence" /> <param name="index_algorithm" type="select" label="Algorithm for constructing BWT index"> <option value="automatic" selected="True" help="1GB cut-off">Guess automatically</option> <option value="is" hel="Small genomes">IS linear-time algorithm</option> <!-- <option value="div">div</option> --> <option value="bwtsw" help="Large genomes">BWT-SW</option> </param> </inputs> <outputs> <data name="out_file" format="data_manager_json"/> </outputs> <help> .. class:: infomark **Notice:** If you leave name, description, or id blank, it will be generated automatically. </help> </tool>