# HG changeset patch
# User elixir-it
# Date 1541697236 18000
# Node ID a28564bf926ad63dd6eb9230b876294cd767fea5

Uploaded

diff -r 000000000000 -r a28564bf926a covacs_annovar.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/covacs_annovar.xml	Thu Nov 08 12:13:56 2018 -0500
@@ -0,0 +1,102 @@
+<tool id="annovar_elixir" name="annovar" version="1">
+  <description> annovar, annotate variants using specified gene annotations, regions, and filtering databases</description>
+  <requirements>
+    <requirement type="package" >perl</requirement>
+  </requirements>
+  <command> <![CDATA[
+       ### call the .sh to untar the package 
+	sh $__tool_directory__/mv_untar_annovar.sh &&
+
+	 ## Variant annotation; make sure to include entry in indexes table for build database.
+
+          #set protocol = []
+          #set operation = []
+
+          ## Add gene annotations.
+          #if $gene_anns:
+              #silent protocol.append( str( $gene_anns )  )
+              #silent operation.append( ','.join( ['g' for t in range( str($gene_anns).count(',') + 1 )] ) )
+          #end if
+           
+          ## Add filters.
+          #if $filters:
+              #silent protocol.append( str( $filters ) )
+              #silent operation.append( ','.join( ['f' for t in range( str($filters).count(',') + 1 )] ) )
+          #end if
+	  ##add resions.
+          #if $regions:
+              #silent protocol.append( str( $regions ) )
+              #silent operation.append( ','.join( ['r' for t in range( str($filters).count(',') + 1 )] ) )
+          #end if
+
+
+          #set protocol = ','.join( $protocol )
+          #set operation = ','.join( $operation )
+
+          ## Annotate variants.
+          perl \$CONDA_PREFIX/annovar/table_annovar.pl  $input1 $location_db.fields.path --buildver $assembly --out annovarAnnotation --protocol $protocol --operation $operation --nastring $NA --vcfinput
+    ]]>
+  </command>
+  <inputs>
+    <param name="assembly" type="select" label="Genome_assembly" multiple="no">
+      <option value="hg18" >hg18</option>
+      <option value="hg19" selected="true">hg19</option>
+      <option value="hg38" >hg38</option>
+    </param>
+    <param name="NA" type="text" label="substitute NA with:"/>
+    <param format="vcf" name="input1" type="data" label="VCF" help="vcf input file"/>
+    <param name="gene_anns" type="select" multiple="yes" optional="true">
+      <options from_data_table="annovar">
+	<filter type="static_value" name="type" value="gene_ann" column="1"/>
+	<filter type="sort_by" column="0"/>
+      </options>
+    </param>
+    <param name="filters" type="select" multiple="yes" optional="true">
+      <options from_data_table="annovar">
+	<filter type="static_value" name="type" value="filter" column="1"/>
+        <filter type="sort_by" column="0"/>
+      </options>
+    </param>
+    <param name="regions" type="select" multiple="yes" optional="true">
+      <options from_data_table="annovar">
+	<filter type="static_value" name="type" value="regions" column="1"/>
+        <filter type="sort_by" column="0"/>
+      </options>
+    </param>
+    <param name="location_db" type="select" display="radio">
+      <options from_data_table="annovar">
+        <filter type="static_value" name="type" value="location" column="1"/>
+        <filter type="sort_by" column="0"/>
+      </options>
+    </param> 
+  </inputs>
+  <outputs>
+    <data format="vcf" name="output" from_work_dir="annovarAnnotation.????_multianno.vcf" label="${tool.name} on ${on_string}"/>
+  </outputs>
+  <stdio>
+    <regex match=".*" source="both" level="log" description="tool progress"/>
+  </stdio>
+  <tests>
+      <test>
+      </test>
+  </tests>
+  <help>
+**What it does**
+
+This tool will annotate variants using specified gene annotations, regions, and filtering databases. Input is a VCF dataset, and output is a table of annotations for each variant in the
+VCF dataset or a VCF dataset with the annotations in INFO fields.
+
+
+**Important Usage Note**
+
+ANNOVAR is open-source and free for non-profit use. If you use it for commercial purposes, please contact BIOBASE (info@biobase-international.com) directly for license related issues. Also see http://www.openbioinformatics.org/annovar/annovar_faq.html#license
+
+**IMPORTANT** to get the wrapper ready to start the admin user have to download annovar."version".tar.gz and then move it in the conda_prefix folder, the path of the conda_prefix is written in the galaxy.ini(or .yml) file
+
+
+  </help>
+  <citations>
+	<citation type="doi">10.1093/nar/gkq603</citation>
+        <citation type="doi">10.1186/s12864-018-4508-1</citation>
+  </citations>
+</tool>
diff -r 000000000000 -r a28564bf926a mv_untar_annovar.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mv_untar_annovar.sh	Thu Nov 08 12:13:56 2018 -0500
@@ -0,0 +1,11 @@
+#!/bin/bash
+# if the symbolic link is not present in the annovar conda virtual environment the script search for the tar.gz in the conda_prefix,
+# untar the archive and make a symbolic link to the $CONDA_PREFIX of the conda virtual environment
+if [[ ! -d $CONDA_PREFIX/annovar ]] ; then
+	tar -zxvf $CONDA_PREFIX/../../annovar.*.tar.gz -C $CONDA_PREFIX/../../ &&
+	echo start untar &&
+	ln -s $CONDA_PREFIX/../../annovar $CONDA_PREFIX &&
+	echo all done
+else
+	echo annovar was present
+fi
diff -r 000000000000 -r a28564bf926a tool-data/annovar.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/annovar.loc.sample	Thu Nov 08 12:13:56 2018 -0500
@@ -0,0 +1,10 @@
+
+#location of humandb the fields are tab delimited 
+db	location	/export/_conda/annovar/humandb
+
+
+
+#definition of present db name + type(gene_ann, region, filter) the fields are tab delimited
+refGene	gene_ann	
+prova	gene_ann	
+exac03	filter		
diff -r 000000000000 -r a28564bf926a tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Nov 08 12:13:56 2018 -0500
@@ -0,0 +1,5 @@
+<!-- Location of annovar_elixir loc file -->
+<table name="annovar" comment_char="#">
+	<columns> value, type, path</columns>
+	<file path="tool-data/annovar.loc" />
+</table>