Mercurial > repos > devteam > data_manager_bwa_mem_index_builder
annotate data_manager/bwa_mem_index_builder.xml @ 4:414a92a973fa draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_mem_index_builder commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
author | devteam |
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date | Thu, 19 Jan 2017 11:48:36 -0500 |
parents | e519769cdb9c |
children | 46066df8813d |
rev | line source |
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4
414a92a973fa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_mem_index_builder commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
3
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changeset
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1 <tool id="bwa_mem_index_builder_data_manager" name="BWA-MEM index" tool_type="manage_data" version="0.0.3"> |
0 | 2 <description>builder</description> |
3 <requirements> | |
4
414a92a973fa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_mem_index_builder commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
parents:
3
diff
changeset
|
4 <requirement type="package" version="0.7.15">bwa</requirement> |
0 | 5 </requirements> |
6 <command interpreter="python">bwa_mem_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_mem_indexes"</command> | |
7 <stdio> | |
8 <exit_code range=":-1" /> | |
9 <exit_code range="1:" /> | |
10 </stdio> | |
11 <inputs> | |
12 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> | |
13 <options from_data_table="all_fasta"/> | |
14 </param> | |
15 <param type="text" name="sequence_name" value="" label="Name of sequence" /> | |
16 <param type="text" name="sequence_id" value="" label="ID for sequence" /> | |
17 | |
18 <param name="index_algorithm" type="select" label="Algorithm for constructing BWT index"> | |
19 <option value="automatic" selected="True" help="2GB cut-off">Guess automatically</option> | |
20 <option value="is" hel="Small genomes">IS linear-time algorithm</option> | |
21 <!-- <option value="div">div</option> --> | |
22 <option value="bwtsw" help="Large genomes">BWT-SW</option> | |
23 </param> | |
24 | |
25 </inputs> | |
26 <outputs> | |
27 <data name="out_file" format="data_manager_json"/> | |
28 </outputs> | |
29 | |
30 <help> | |
31 | |
32 .. class:: infomark | |
33 | |
34 **Notice:** If you leave name, description, or id blank, it will be generated automatically. | |
35 | |
36 </help> | |
37 </tool> |