|
0
|
1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="0.0.1">
|
|
|
2 <description>bowtie2 index builder</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="2.1.0">bowtie</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 <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>
|
