Mercurial > repos > jjohnson > data_manager_bowtie2_index_builder
view data_manager/bowtie2_index_builder.xml @ 0:5515ee3559f0 draft default tip
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author | jjohnson |
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date | Tue, 20 Aug 2013 11:58:27 -0400 |
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<tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="0.0.1"> <description>bowtie2 index builder</description> <requirements> <requirement type="package" version="2.1.0">bowtie</requirement> </requirements> <command interpreter="python">bowtie2_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 "bowtie2_indexes"</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" help="Leave blank to use all_fasta name" /> <param type="text" name="sequence_id" value="" label="ID for sequence" help="Leave blank to use all_fasta id" /> </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>