Mercurial > repos > devteam > data_manager_picard_index_builder

comparison data_manager/picard_index_builder.xml @ 1:dc28cd6a1d44 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
author iuc
date Tue, 04 Apr 2017 18:12:10 -0400
parents 00491eabe22b
children ae080ff506fd
comparison
equal deleted inserted replaced
0:00491eabe22b 1:dc28cd6a1d44
1 <tool id="picard_index_builder_data_manager" name="Picard index" tool_type="manage_data" version="0.0.1"> 1 <tool id="picard_index_builder_data_manager" name="Picard index" tool_type="manage_data" version="2.7.1">
2 <description>builder</description> 2 <description>builder</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.56.0">picard</requirement> 4 <requirement type="package" version="2.7.1">picard</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python">picard_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 "picard_indexes"</command> 6 <command detect_errors="exit_code"><![CDATA[
7 <stdio> 7 python '$__tool_directory__/picard_index_builder.py'
8 <exit_code range=":-1" /> 8 '${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 picard_indexes
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 </inputs> 20 </inputs>
18 <outputs> 21 <outputs>
19 <data name="out_file" format="data_manager_json"/> 22 <data name="out_file" format="data_manager_json"/>
20 </outputs> 23 </outputs>
21 24
22 <help> 25 <help>
23
24 .. class:: infomark 26 .. class:: infomark
25 27
26 **Notice:** If you leave name, description, or id blank, it will be generated automatically. 28 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
27
28 </help> 29 </help>
29 </tool> 30 </tool>