Mercurial > repos > jjohnson > data_manager_hisat_index_builder
diff data_manager/hisat_index_builder.xml @ 0:4c7db9cbbbf7 draft default tip
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author | jjohnson |
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date | Tue, 22 Jul 2014 08:52:53 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/hisat_index_builder.xml Tue Jul 22 08:52:53 2014 -0400 @@ -0,0 +1,25 @@ +<tool id="hisat_index_builder_data_manager" name="HISAT index" tool_type="manage_data" version="0.0.1"> + <description>hisat index builder</description> + <requirements> + <requirement type="package" version="0.1.0-beta">hisat</requirement> + </requirements> + <command interpreter="python">hisat_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 "hisat_indexes"</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" /> + </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>