Mercurial > repos > devteam > data_manager_bowtie2_index_builder
view data_manager/bowtie2_index_builder.xml @ 9:47432d88b0a0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 9fa01fe96452d50646e066066b1e556ba4a75ced"
author | iuc |
---|---|
date | Mon, 06 Apr 2020 23:13:03 +0000 |
parents | 62f1a6310409 |
children | 2699da480b0b |
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<tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="@WRAPPER_VERSION@.1+galaxy1" profile="18.09"> <description>builder</description> <requirements> <requirement type="package" version="@WRAPPER_VERSION@">bowtie2</requirement> </requirements> <macros> <token name="@WRAPPER_VERSION@">2.3.5</token> </macros> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/bowtie2_index_builder.py' '${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 bowtie2_indexes ${tophat2} ]]></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="tophat2" type="boolean" truevalue="--data_table_name tophat2_indexes" falsevalue="" checked="True" label="Also make available for TopHat" help="Adds values to tophat2_indexes tool data table" /> </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="bowtie2_data_manager.json"/> </test> </tests> <help> .. class:: infomark **Notice:** If you leave name, description, or id blank, it will be generated automatically. </help> </tool>