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comparison data_manager/twobit_builder.xml @ 2:9946bc39c834 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
author iuc
date Tue, 04 Apr 2017 18:16:29 -0400
parents df883cc67fbd
children 5c77d4091880
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1:df883cc67fbd 2:9946bc39c834
1 <tool id="twobit_builder_data_manager" name="TwoBit" tool_type="manage_data" version="0.0.2"> 1 <tool id="twobit_builder_data_manager" name="TwoBit" tool_type="manage_data" version="0.0.2">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="324">ucsc-fatotwobit</requirement> 3 <requirement type="package" version="324">ucsc-fatotwobit</requirement>
4 </requirements> 4 </requirements>
5 <description>builder</description> 5 <description>builder</description>
6 <command interpreter="python">twobit_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}"</command> 6 <command detect_errors="exit_code"><![CDATA[
7 python '$__tool_directory__/twobit_builder.py'
8 '${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 ]]></command>
7 <inputs> 13 <inputs>
8 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> 14 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
9 <options from_data_table="all_fasta"/> 15 <options from_data_table="all_fasta"/>
10 </param> 16 </param>
11 <param type="text" name="sequence_name" value="" label="Name of sequence" /> 17 <param name="sequence_name" type="text" value="" label="Name of sequence" />
12 <param type="text" name="sequence_id" value="" label="ID for sequence" /> 18 <param name="sequence_id" type="text" value="" label="ID for sequence" />
13
14 </inputs> 19 </inputs>
15 <outputs> 20 <outputs>
16 <data name="out_file" format="data_manager_json"/> 21 <data name="out_file" format="data_manager_json"/>
17 </outputs> 22 </outputs>
18 23
23 <output name="sequence_id" file="data_manager_two_bit_out_1.dat"/> 28 <output name="sequence_id" file="data_manager_two_bit_out_1.dat"/>
24 </test> 29 </test>
25 </tests> 30 </tests>
26 31
27 <help> 32 <help>
28
29 .. class:: infomark 33 .. class:: infomark
30 34
31 **Notice:** If you leave name, description, or id blank, it will be generated automatically. 35 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
32
33 </help> 36 </help>
34 </tool> 37 </tool>
35 38