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comparison snpEff_create_db.xml @ 13:f0ee2b470481 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 0310c734a944901fffb975937b20f55bfc1d9f46
author iuc
date Sat, 07 Apr 2018 15:46:09 -0400
parents 5a29ab10dba6
children 479c4f2f4826
comparison
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12:5a29ab10dba6 13:f0ee2b470481
1 <tool id="snpEff_build_gb" name="SnpEff build:" version="@wrapper_version@.galaxy1"> 1 <tool id="snpEff_build_gb" name="SnpEff build:" version="@wrapper_version@.galaxy2">
2 <description> database from Genbank record</description> 2 <description> database from Genbank record</description>
3 <macros> 3 <macros>
4 <import>snpEff_macros.xml</import> 4 <import>snpEff_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
27 ln -s '${input_gbk}' '${snpeff_output.files_path}'/'${genome_version}'/genes.gbk && 27 ln -s '${input_gbk}' '${snpeff_output.files_path}'/'${genome_version}'/genes.gbk &&
28 28
29 snpEff @java_options@ build -v 29 snpEff @java_options@ build -v
30 -configOption '${genome_version}'.genome='${genome_version}' 30 -configOption '${genome_version}'.genome='${genome_version}'
31 -configOption '${genome_version}'.codonTable='${codon_table}' 31 -configOption '${genome_version}'.codonTable='${codon_table}'
32 -genbank -dataDir '$snpeff_output.files_path' '$genome_version' 32 -genbank -dataDir '${snpeff_output.files_path}' '${genome_version}' &&
33 echo "${genome_version}.genome : ${genome_version}" >> '${snpeff_output.files_path}'/snpEff.config &&
34 echo "${genome_version}.codonTable : ${codon_table}" >> '${snpeff_output.files_path}'/snpEff.config
33 35
34 ]]></command> 36 ]]></command>
35 <inputs> 37 <inputs>
36 <param name="genome_version" type="text" value="" label="Name for the database" help="for E. coli K12 you may want to use 'EcK12' etc."> 38 <param name="genome_version" type="text" value="" label="Name for the database" help="for E. coli K12 you may want to use 'EcK12' etc.">
37 <validator type="regex" message="A genome version name is required">\S+</validator> 39 <validator type="regex" message="A genome version name is required">\S+</validator>