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comparison dante.xml @ 3:18d6c1c66798 draft

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author petr-novak
date Wed, 03 Jul 2019 05:09:48 -0400
parents 77d9f2ecb28a
children 6dcecbe81d78
comparison
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2:e2389cdb9b1f 3:18d6c1c66798
1 <tool id="dante" name="Domain based ANnotation of Transposable Elements - DANTE" version="1.0.0"> 1 <tool id="dante" name="Domain based ANnotation of Transposable Elements - DANTE" version="1.0.0">
2 <description> Tool for annotation of transposable elements based on the similarity to conserved protein domains database. </description> 2 <description> Tool for annotation of transposable elements based on the similarity to conserved protein domains database. </description>
3 <requirements> 3 <requirements>
4 <requirement type="package">last</requirement> 4 <requirement type="package">last</requirement>
5 <requirement type="package">numpy</requirement> 5 <requirement type="package">numpy</requirement>
6 <requirement type="package" version="1.0">rexdb</requirement>
6 </requirements> 7 </requirements>
7 <stdio> 8 <stdio>
8 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> 9 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
9 <regex match="error" source="stderr" level="fatal" description="Unknown error" /> 10 <regex match="error" source="stderr" level="fatal" description="Unknown error" />
10 </stdio> 11 </stdio>
11 <command> 12 <command>
12 python3 ${__tool_directory__}/dante.py --query ${input} --domain_gff ${DomGff} 13 python3 ${__tool_directory__}/dante.py --query ${input} --domain_gff ${DomGff}
13 --protein_database ${__tool_directory__ }/tool-data/protein_domains/${db_type}_pdb 14 --protein_database \${REXDB}/${db_type}_pdb
14 --classification ${__tool_directory__ }/tool-data/protein_domains/${db_type}_class 15 --classification ${__tool_directory__ }/tool-data/protein_domains/${db_type}_class
15 </command> 16 </command>
16 <inputs> 17 <inputs>
17 <param format="fasta" type="data" name="input" label="Choose your input sequence" help="Input DNA must be in proper fasta format, multi-fasta containing more sequences is allowed" /> 18 <param format="fasta" type="data" name="input" label="Choose your input sequence" help="Input DNA must be in proper fasta format, multi-fasta containing more sequences is allowed" />
18 19