# HG changeset patch
# User morinlab
# Date 1485553767 18000
# Node ID 352ec92784742901f3338169d5a3dea419815838
# Parent  197ea6c746b0cf9bd36f61963d171c17c9771c1c
Deleted selected files

diff -r 197ea6c746b0 -r 352ec9278474 download_genome.xml
--- a/download_genome.xml	Fri Jan 27 16:43:27 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-<tool id="download_genome" name="Get Genome" version="1.0.0">
-    <description>
-      Download and Index Genomes using Ensemble VEP
-    </description>
-    <requirements>
-        <requirement type="package" version="84">ensembl_vep</requirement>
-    </requirements>    
-    <command>
-	perl \$ENSEMBL_VEP_84_INSTALL_DIR/INSTALL.pl 
-		--AUTO cf 
-		--SPECIES \$(echo $species_select.value | sed 's/-/\t/g' | cut -f1) 
-		--CACHEDIR \$ENSEMBL_VEP_84_INSTALL_DIR/cache
-		#if "-" in $species_select.value
-		  --ASSEMBLY \$(echo $species_select.value | sed 's/-/\t/g' | cut -f2)
-		#end if
-        ;
-        
-        gzip -d \$ENSEMBL_VEP_84_INSTALL_DIR/cache/\$(echo $species_select.value | sed 's/-/\t/g' | cut -f1 | sed 's/\ /_/g')/*\$(echo $species_select.value | sed 's/-/\t/g' | cut -f2)/*.fa.gz;
-      	samtools faidx \$ENSEMBL_VEP_84_INSTALL_DIR/cache/\$(echo $species_select.value | sed 's/-/\t/g' | cut -f1 | sed 's/\ /_/g')/*\$(echo $species_select.value | sed 's/-/\t/g' | cut -f2)/*.fa;
-	
-	env > $output;
-   </command>
-    <inputs>
-      <expand macro="genome_list" />
-    </inputs>
-    <outputs>
-        <data format="txt" name="output"/>
-    </outputs>
-    <stdio>
-        <exit_code range="1:" level="fatal" description="Failure" />
-    </stdio>
-    <macros>
-      <import>ensembl_vep_macros.xml</import>
-    </macros>
-    
-</tool>