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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit eb0405e83bae7b6f11446236044a6aed2fcaf4d6"
author matthias
date Thu, 02 Apr 2020 13:16:53 +0000
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1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="@WRAPPER_VERSION@.1+galaxy1" profile="18.09">
2 <description>builder</description>
3 <requirements>
4 <requirement type="package" version="@WRAPPER_VERSION@">bowtie2</requirement>
5 </requirements>
6 <macros>
7 <token name="@WRAPPER_VERSION@">2.3.5</token>
8 </macros>
9 <command detect_errors="exit_code"><![CDATA[
10 python '$__tool_directory__/bowtie2_index_builder.py'
11 '${out_file}'
12 --fasta_filename '${all_fasta_source.fields.path}'
13 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
14 --fasta_description '${all_fasta_source.fields.name}'
15 --data_table_name bowtie2_indexes ${tophat2}
16 ]]></command>
17 <inputs>
18 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
19 <options from_data_table="all_fasta"/>
20 </param>
21 <param name="sequence_name" type="text" value="" label="Name of sequence" />
22 <param name="sequence_id" type="text" value="" label="ID for sequence" />
23 <param name="tophat2" type="boolean" truevalue="--data_table_name tophat2_indexes" falsevalue="" checked="True" label="Also make available for TopHat" help="Adds values to tophat2_indexes tool data table" />
24 </inputs>
25 <outputs>
26 <data name="out_file" format="data_manager_json"/>
27 </outputs>
28 <tests>
29 <test>
30 <param name="all_fasta_source" value="phiX174"/>
31 <output name="out_file" value="bowtie2_data_manager.json"/>
32 </test>
33 </tests>
34
35 <help>
36 .. class:: infomark
37
38 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
39 </help>
40 </tool>