Mercurial > repos > devteam > data_manager_bwa_mem_index_builder
view data_manager/bwa_mem_index_builder.xml @ 9:9e993022c762 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 096286097ed5cdf189a1b68c3fc34d10f4142e54
author | iuc |
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date | Sun, 16 Apr 2023 08:29:59 +0000 |
parents | 37580590ecfb |
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<tool id="bwa_mem_index_builder_data_manager" name="BWA-MEM index" tool_type="manage_data" version="0.0.5" profile="19.05"> <description>builder</description> <requirements> <requirement type="package" version="0.7.17">bwa</requirement> <requirement type="package" version="3.7">python</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/bwa_mem_index_builder.py' '${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_mem_indexes ]]></command> <inputs> <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> <options from_data_table="all_fasta"/> </param> <param name="sequence_name" type="text" value="" label="Name of sequence" /> <param name="sequence_id" type="text" value="" label="ID for sequence" /> <param name="index_algorithm" type="select" label="Algorithm for constructing BWT index"> <option value="automatic" selected="true">Guess automatically (2GB cut-off)</option> <option value="is">IS linear-time algorithm (for small genomes)</option> <option value="bwtsw">BWT-SW (for large genomes)</option> </param> </inputs> <outputs> <data name="out_file" format="data_manager_json"/> </outputs> <tests> <test> <param name="all_fasta_source" value="phiX174"/> <output name="out_file" value="bwa_mem_data_manager.json"/> </test> </tests> <help> .. class:: infomark **Notice:** If you leave name, description, or id blank, it will be generated automatically. </help> </tool>