Mercurial > repos > iuc > snpeff

diff 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
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--- a/snpEff_create_db.xml	Thu Mar 29 20:39:49 2018 -0400
+++ b/snpEff_create_db.xml	Sat Apr 07 15:46:09 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="snpEff_build_gb" name="SnpEff build:" version="@wrapper_version@.galaxy1">
+<tool id="snpEff_build_gb" name="SnpEff build:" version="@wrapper_version@.galaxy2">
     <description> database from Genbank record</description>
     <macros>
         <import>snpEff_macros.xml</import>
@@ -29,7 +29,9 @@
         snpEff @java_options@ build -v
         -configOption '${genome_version}'.genome='${genome_version}'
         -configOption '${genome_version}'.codonTable='${codon_table}'
-        -genbank -dataDir '$snpeff_output.files_path' '$genome_version'
+        -genbank -dataDir '${snpeff_output.files_path}' '${genome_version}' &&
+        echo "${genome_version}.genome : ${genome_version}" >> '${snpeff_output.files_path}'/snpEff.config &&
+        echo "${genome_version}.codonTable : ${codon_table}" >> '${snpeff_output.files_path}'/snpEff.config
 
     ]]></command>
     <inputs>