Mercurial > repos > jjohnson > data_manager_hisat_index_builder
comparison 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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-1:000000000000 | 0:4c7db9cbbbf7 |
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1 <tool id="hisat_index_builder_data_manager" name="HISAT index" tool_type="manage_data" version="0.0.1"> | |
2 <description>hisat index builder</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.1.0-beta">hisat</requirement> | |
5 </requirements> | |
6 <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> | |
7 <inputs> | |
8 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> | |
9 <options from_data_table="all_fasta"/> | |
10 </param> | |
11 <param type="text" name="sequence_name" value="" label="Name of sequence" help="Leave blank to use all_fasta name" /> | |
12 <param type="text" name="sequence_id" value="" label="ID for sequence" help="Leave blank to use all_fasta id" /> | |
13 </inputs> | |
14 <outputs> | |
15 <data name="out_file" format="data_manager_json"/> | |
16 </outputs> | |
17 | |
18 <help> | |
19 | |
20 .. class:: infomark | |
21 | |
22 **Notice:** If you leave name, description, or id blank, it will be generated automatically. | |
23 | |
24 </help> | |
25 </tool> |