Mercurial > repos > iuc > data_manager_bowtie_index_builder

comparison data_manager/bowtie_index_builder.xml @ 4:86e9af693a33 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae
author iuc
date Fri, 09 Jun 2017 06:12:02 -0400
parents 086edfff112b
children 39a922d01b0d
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3:ea5faedd0795 4:86e9af693a33
1 <tool id="bowtie_index_builder_data_manager" name="Bowtie index" tool_type="manage_data" version="0.0.3"> 1 <tool id="bowtie_index_builder_data_manager" name="Bowtie index" tool_type="manage_data" version="1.2.0">
2 <description>builder</description> 2 <description>builder</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1.2">bowtie</requirement> 4 <requirement type="package" version="1.2.0">bowtie</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python"> 6 <command detect_errors="exit_code"><![CDATA[
7 bowtie_index_builder.py 7 python '$__tool_directory__/bowtie_index_builder.py'
8 "${out_file}" 8 '${out_file}'
9 --fasta_filename "${all_fasta_source.fields.path}" 9 --fasta_filename '${all_fasta_source.fields.path}'
10 --fasta_dbkey "${all_fasta_source.fields.dbkey}" 10 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
11 --fasta_description "${all_fasta_source.fields.name}" 11 --fasta_description '${all_fasta_source.fields.name}'
12 --data_table_name "bowtie_indexes" 12 --data_table_name bowtie_indexes
13 </command> 13 ]]></command>
14 <inputs> 14 <inputs>
15 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> 15 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
16 <options from_data_table="all_fasta"/> 16 <options from_data_table="all_fasta"/>
17 </param> 17 </param>
18 <param type="text" name="sequence_name" value="" label="Name of sequence" help="Leave blank to use all_fasta name" /> 18 <param name="sequence_name" type="text" value="" label="Name of sequence" help="Leave blank to use all_fasta name" />
19 <param type="text" name="sequence_id" value="" label="ID for sequence" help="Leave blank to use all_fasta id "/> 19 <param name="sequence_id" type="text" value="" label="ID for sequence" help="Leave blank to use all_fasta id" />
20 </inputs> 20 </inputs>
21 <outputs> 21 <outputs>
22 <data name="out_file" format="data_manager_json"/> 22 <data name="out_file" format="data_manager_json"/>
23 </outputs> 23 </outputs>
24 <help> 24 <help><![CDATA[
25
26 .. class:: infomark 25 .. class:: infomark
27 26
28 **Notice:** If you leave name, description, or id blank, it will be generated automatically. 27 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
29 28 ]]></help>
30 </help> 29 <citations>
30 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
31 </citations>
31 </tool> 32 </tool>