Mercurial > repos > devteam > data_manager_gatk_picard_index_builder
view data_manager/data_manager_gatk_picard_index_builder.xml @ 3:b31f1fcb203c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gatk_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
author | iuc |
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date | Tue, 04 Apr 2017 18:08:38 -0400 |
parents | 700f2df51eb0 |
children | 0f85d523291e |
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<tool id="gatk_picard_index_builder" name="Generate GATK-sorted Picard indexes" tool_type="manage_data" version="0.0.1"> <description>builder</description> <requirements> <requirement type="package" version="0.1.18">samtools</requirement> <requirement type="package" version="1.56.0">picard</requirement> </requirements> <command detect_errors="exit_code"> python '$__tool_directory__/data_manager_gatk_picard_index_builder.py' '${out_file}' --jar "\$JAVA_JAR_PATH/CreateSequenceDictionary.jar" --fasta_filename '${all_fasta_source.fields.path}' --fasta_dbkey '${all_fasta_source.fields.dbkey}' --fasta_description '${all_fasta_source.fields.name}' --data_table_name gatk_picard_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" /> </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>