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comparison snpEff_create_db.xml @ 12:5a29ab10dba6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a69e15a4016b3088ec937d6f2349be091c6b1b71
author iuc
date Thu, 29 Mar 2018 20:39:49 -0400
parents bfa6c1b8a03c
children f0ee2b470481
comparison
equal deleted inserted replaced
11:bfa6c1b8a03c 12:5a29ab10dba6
1 <tool id="snpEff_build_gb" name="SnpEff build:" version="@wrapper_version@.1"> 1 <tool id="snpEff_build_gb" name="SnpEff build:" version="@wrapper_version@.galaxy1">
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>
21 #end if 21 #end if
22 && 22 &&
23 #end if 23 #end if
24 24
25 mkdir -p '${snpeff_output.files_path}'/'${genome_version}' && 25 mkdir -p '${snpeff_output.files_path}'/'${genome_version}' &&
26 26
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 33
34 ]]></command> 34 ]]></command>
35 <inputs> 35 <inputs>