comparison data_manager/bwa_index_builder.xml @ 0:ae10d0ddbbb1 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
author devteam
date Fri, 06 Nov 2015 14:15:00 -0500
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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 <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="1GB 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>