Mercurial > repos > devteam > data_manager_bwa_index_builder
diff data_manager/bwa_index_builder.xml @ 0:ae10d0ddbbb1 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
author | devteam |
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date | Fri, 06 Nov 2015 14:15:00 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/bwa_index_builder.xml Fri Nov 06 14:15:00 2015 -0500 @@ -0,0 +1,37 @@ +<tool id="bwa_index_builder_data_manager" name="BWA 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"</command> + <stdio> + <exit_code range=":-1" /> + <exit_code range="1:" /> + </stdio> + <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>