comparison data_manager/bowtie2_index_builder.xml @ 0:9458af1ab90b draft

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author devteam
date Tue, 14 Apr 2015 12:06:01 -0400
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1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="0.0.1">
2 <description>builder</description>
3 <requirements>
4 <requirement type="package" version="2.2.4">bowtie2</requirement>
5 </requirements>
6 <command interpreter="python">bowtie2_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 "bowtie2_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 </inputs>
18 <outputs>
19 <data name="out_file" format="data_manager_json"/>
20 </outputs>
21
22 <help>
23
24 .. class:: infomark
25
26 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
27
28 </help>
29 </tool>