Mercurial > repos > devteam > data_manager_bowtie2_index_builder
diff data_manager/bowtie2_index_builder.xml @ 5:8a892275932f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
author | iuc |
---|---|
date | Tue, 04 Apr 2017 17:48:28 -0400 |
parents | 49331eedb1c5 |
children | bb050998cee2 |
line wrap: on
line diff
--- a/data_manager/bowtie2_index_builder.xml Fri Dec 18 18:29:59 2015 -0500 +++ b/data_manager/bowtie2_index_builder.xml Tue Apr 04 17:48:28 2017 -0400 @@ -1,30 +1,31 @@ -<tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="2.2.6"> +<tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="2.3.0"> <description>builder</description> <requirements> - <requirement type="package" version="2.2.6">bowtie2</requirement> + <requirement type="package" version="2.3.0">bowtie2</requirement> </requirements> - <command interpreter="python">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" ${tophat2}</command> - <stdio> - <exit_code range=":-1" /> - <exit_code range="1:" /> - </stdio> + <command detect_errors="exit_code"><![CDATA[ + python '$__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 type="text" name="sequence_name" value="" label="Name of sequence" /> - <param type="text" name="sequence_id" value="" label="ID for sequence" /> - <param type="boolean" name="tophat2" label="Also make available for TopHat" checked="True" truevalue="--data_table_name tophat2_indexes" falsevalue="" help="Adds values to tophat2_indexes tool data table." /> + <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> <help> - .. class:: infomark -**Notice:** If you leave name, description, or id blank, it will be generated automatically. - +**Notice:** If you leave name, description, or id blank, it will be generated automatically. </help> </tool>