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comparison data_manager/bowtie2_index_builder.xml @ 5:8a892275932f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
author iuc
date Tue, 04 Apr 2017 17:48:28 -0400
parents 49331eedb1c5
children bb050998cee2
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4:c85369954c54 5:8a892275932f
1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="2.2.6"> 1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="2.3.0">
2 <description>builder</description> 2 <description>builder</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.2.6">bowtie2</requirement> 4 <requirement type="package" version="2.3.0">bowtie2</requirement>
5 </requirements> 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" ${tophat2}</command> 6 <command detect_errors="exit_code"><![CDATA[
7 <stdio> 7 python '$__tool_directory__/bowtie2_index_builder.py'
8 <exit_code range=":-1" /> 8 '${out_file}'
9 <exit_code range="1:" /> 9 --fasta_filename '${all_fasta_source.fields.path}'
10 </stdio> 10 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
11 --fasta_description '${all_fasta_source.fields.name}'
12 --data_table_name bowtie2_indexes ${tophat2}
13 ]]></command>
11 <inputs> 14 <inputs>
12 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> 15 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
13 <options from_data_table="all_fasta"/> 16 <options from_data_table="all_fasta"/>
14 </param> 17 </param>
15 <param type="text" name="sequence_name" value="" label="Name of sequence" /> 18 <param name="sequence_name" type="text" value="" label="Name of sequence" />
16 <param type="text" name="sequence_id" value="" label="ID for sequence" /> 19 <param name="sequence_id" type="text" value="" label="ID for sequence" />
17 <param type="boolean" name="tophat2" label="Also make available for TopHat" checked="True" truevalue="--data_table_name tophat2_indexes" falsevalue="" help="Adds values to tophat2_indexes tool data table." /> 20 <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" />
18 </inputs> 21 </inputs>
19 <outputs> 22 <outputs>
20 <data name="out_file" format="data_manager_json"/> 23 <data name="out_file" format="data_manager_json"/>
21 </outputs> 24 </outputs>
22 25
23 <help> 26 <help>
24
25 .. class:: infomark 27 .. class:: infomark
26 28
27 **Notice:** If you leave name, description, or id blank, it will be generated automatically. 29 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
28
29 </help> 30 </help>
30 </tool> 31 </tool>