Mercurial > repos > iuc > data_manager_bowtie_index_builder
diff data_manager/bowtie_color_space_index_builder.xml @ 4:86e9af693a33 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
author | iuc |
---|---|
date | Fri, 09 Jun 2017 06:12:02 -0400 |
parents | 086edfff112b |
children | 39a922d01b0d |
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--- a/data_manager/bowtie_color_space_index_builder.xml Tue Apr 04 18:06:27 2017 -0400 +++ b/data_manager/bowtie_color_space_index_builder.xml Fri Jun 09 06:12:02 2017 -0400 @@ -1,32 +1,33 @@ -<tool id="bowtie_color_space_index_builder_data_manager" name="Bowtie Color index" tool_type="manage_data" version="0.0.3"> +<tool id="bowtie_color_space_index_builder_data_manager" name="Bowtie Color index" tool_type="manage_data" version="1.2.0"> <description>builder</description> <requirements> - <requirement type="package" version="1.1.2">bowtie</requirement> + <requirement type="package" version="1.2.0">bowtie</requirement> </requirements> - <command interpreter="python"> - bowtie_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 "bowtie_indexes_color" - --color_space - </command> + <command detect_errors="exit_code"><![CDATA[ +python '$__tool_directory__/bowtie_index_builder.py' +'${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 bowtie_indexes_color +--color_space + ]]></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" help="Leave blank to use all_fasta name" /> - <param type="text" name="sequence_id" value="" label="ID for sequence" help="Leave blank to use all_fasta id" /> + <param name="sequence_name" type="text" value="" label="Name of sequence" help="Leave blank to use all_fasta name" /> + <param name="sequence_id" type="text" value="" label="ID for sequence" help="Leave blank to use all_fasta id" /> </inputs> <outputs> <data name="out_file" format="data_manager_json"/> </outputs> - <help> - + <help><![CDATA[ .. class:: infomark -**Notice:** If you leave name, description, or id blank, it will be generated automatically. - - </help> +**Notice:** If you leave name, description, or id blank, it will be generated automatically. + ]]></help> + <citations> + <citation type="doi">10.1186/gb-2009-10-3-r25</citation> + </citations> </tool>