Mercurial > repos > petr-novak > dante

diff dante_gff_to_dna.xml @ 19:b34483adf8f0 draft

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Uploaded
author petr-novak
date Tue, 24 Sep 2019 08:00:54 -0400
parents 039c45c01b47
children 31449f1183d8
line wrap: on
line diff
--- a/dante_gff_to_dna.xml	Tue Sep 24 07:27:56 2019 -0400
+++ b/dante_gff_to_dna.xml	Tue Sep 24 08:00:54 2019 -0400
@@ -2,6 +2,7 @@
   <description> Tool to extract nucleotide sequences of protein domains found by DANTE </description>
   <requirements>
     <requirement type="package">biopython</requirement>
+    <requirement type="set_environment">REXDB</requirement>
   </requirements>
   <command>
     TEMP_DIR_LINEAGES=\$(mktemp -d) &amp;&amp;
@@ -12,7 +13,7 @@
     #else:
 	  --extended False
     #end if
-	  --classification ${__tool_data_path__ }/protein_domains/${db_type}_class
+	  --classification \${REXDB}/${db_type}_class
     &amp;&amp;
 
     cat \$TEMP_DIR_LINEAGES/domains_counts.txt \$TEMP_DIR_LINEAGES/*fasta > $out_fasta &amp;&amp;