Mercurial > repos > devteam > data_manager_sam_fasta_index_builder
view data_manager/data_manager_sam_fasta_index_builder.xml @ 8:3ec5c51384e6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 20381ede5940c6bbca00b550e01550f5aad0f2b7"
author | iuc |
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date | Mon, 01 Nov 2021 08:32:15 +0000 |
parents | f8418a1bf7d0 |
children | a256278e5bff |
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<tool id="sam_fasta_index_builder" name="SAM FASTA index" tool_type="manage_data" version="0.0.5" profile="19.05"> <description>builder</description> <requirements> <requirement type="package" version="1.14">samtools</requirement> <requirement type="package" version="3.7">python</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/data_manager_sam_fasta_index_builder.py' '${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 fasta_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> <tests> <test> <param name="all_fasta_source" value="phiX174"/> <output name="out_file" value="sam_fasta_data_manager.json"/>" </test> </tests> <help> .. class:: infomark **Notice:** If you leave name, description, or id blank, it will be generated automatically. </help> </tool>