Mercurial > repos > iuc > data_manager_sailfish_index_builder
view data_manager/bwa_index_builder.xml @ 0:eae04baa35a6 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sailfish_index_builder commit 418f745190d77983c3fb09badb6298493bccf4e0
author | iuc |
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date | Tue, 05 Jan 2016 12:58:16 -0500 |
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<tool id="sailfish_index_builder_data_manager" name="Sailfish index" tool_type="manage_data" version="0.0.1"> <description>builder</description> <requirements> <requirement type="package" version="0.6.3">sailfish</requirement> </requirements> <command interpreter="python"> sailfish_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 "sailfish_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" /> <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>