Mercurial > repos > devteam > data_manager_bwa_index_builder
comparison data_manager/bwa_index_builder.xml @ 0:367878cb3698 draft
Uploaded data manager definition.
author | devteam |
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date | Fri, 28 Mar 2014 14:18:43 -0400 |
parents | |
children | cc5ae94acf01 |
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-1:000000000000 | 0:367878cb3698 |
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1 <tool id="bwa_index_builder_data_manager" name="BWA index" tool_type="manage_data" version="0.0.1"> | |
2 <description>builder</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.5.9">bwa</requirement> | |
5 </requirements> | |
6 <command interpreter="python">bwa_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 "bwa_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" /> | |
12 <param type="text" name="sequence_id" value="" label="ID for sequence" /> | |
13 | |
14 <param name="index_algorithm" type="select" label="Algorithm for constructing BWT index"> | |
15 <option value="automatic" selected="True" help="1GB cut-off">Guess automatically</option> | |
16 <option value="is" hel="Small genomes">IS linear-time algorithm</option> | |
17 <!-- <option value="div">div</option> --> | |
18 <option value="bwtsw" help="Large genomes">BWT-SW</option> | |
19 </param> | |
20 | |
21 </inputs> | |
22 <outputs> | |
23 <data name="out_file" format="data_manager_json"/> | |
24 </outputs> | |
25 | |
26 <help> | |
27 | |
28 .. class:: infomark | |
29 | |
30 **Notice:** If you leave name, description, or id blank, it will be generated automatically. | |
31 | |
32 </help> | |
33 </tool> |