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comparison data_manager/data_manager_sam_fasta_index_builder.xml @ 3:1f54e98616af draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
author iuc
date Tue, 04 Apr 2017 18:13:56 -0400
parents cf875cbe2df4
children 1865e693d8b2
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2:2a1ac1abc3f7 3:1f54e98616af
1 <tool id="sam_fasta_index_builder" name="SAM FASTA index" tool_type="manage_data" version="0.0.2"> 1 <tool id="sam_fasta_index_builder" name="SAM FASTA index" tool_type="manage_data" version="0.0.2">
2 <description>builder</description> 2 <description>builder</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.1.19">samtools</requirement> 4 <requirement type="package" version="0.1.19">samtools</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python">data_manager_sam_fasta_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 "fasta_indexes"</command> 6 <command detect_errors="exit_code"><![CDATA[
7 python '$__tool_directory__/data_manager_sam_fasta_index_builder.py'
8 '${out_file}'
9 --fasta_filename '${all_fasta_source.fields.path}'
10 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
11 --fasta_description '${all_fasta_source.fields.name}'
12 --data_table_name fasta_indexes
13 ]]></command>
7 <inputs> 14 <inputs>
8 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> 15 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
9 <options from_data_table="all_fasta"/> 16 <options from_data_table="all_fasta"/>
10 </param> 17 </param>
11 <param type="text" name="sequence_name" value="" label="Name of sequence" /> 18 <param name="sequence_name" type="text" value="" label="Name of sequence" />
12 <param type="text" name="sequence_id" value="" label="ID for sequence" /> 19 <param name="sequence_id" type="text" value="" label="ID for sequence" />
13 </inputs> 20 </inputs>
14 <outputs> 21 <outputs>
15 <data name="out_file" format="data_manager_json"/> 22 <data name="out_file" format="data_manager_json"/>
16 </outputs> 23 </outputs>
17 24
18 <help> 25 <help>
19
20 .. class:: infomark 26 .. class:: infomark
21 27
22 **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.
23
24 </help> 29 </help>
25 </tool> 30 </tool>