--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vep_unico.xml	Tue Jul 03 04:38:21 2018 -0400
@@ -0,0 +1,120 @@
+<tool id="vep-unico" name="vep-unico" version="1.0.0">
+    <description>
+        wrapper for variant-effect-predictor86 and vcf2maf
+    </description>
+    <macros>
+        <import>vep-unico-macros.xml</import>
+        <import>vcf2maf-macros.xml</import>
+        <import>vep-download-cache-macros.xml</import>
+        <import>vep-annotate-macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="86">variant-effect-predictor</requirement>
+	<requirement type="package" version="1.3.1">samtools</requirement>
+    </requirements>
+    <command><![CDATA[
+	#if str($veptools.veptoolsselect) =="downloadcache"
+	
+	cd \$CONDA_DEFAULT_ENV && [[ -d vep_cache ]] || mkdir vep_cache ;
+                      cd bin && perl vep_install.pl
+                        -a  ac -s $veptools.species
+                        --NO_HTSLIB
+                        --CACHEDIR \$CONDA_DEFAULT_ENV/vep_cache;
+                        ## write the cache file downloaded 
+                        echo "CACHE DOWNLOADED YET">$output1;
+                        ls \$CONDA_DEFAULT_ENV/vep_cache/*/ >> $output1;
+	#end if
+
+	
+	#if str($veptools.veptoolsselect) =="annotate"
+	 perl \$CONDA_DEFAULT_ENV/bin/variant_effect_predictor.pl
+        --fork \${GALAXY_SLOTS:-4}
+        --offline
+        --dir \$CONDA_DEFAULT_ENV/vep_cache
+        --force_overwrite
+           #if $veptools.everything.value
+           --everything
+           #end if
+        --species $veptools.species
+        --buffer_size $veptools.buffer
+        --vcf
+        --input_file $veptools.input
+        --output_file $output2
+        --stats_file stat.htm 
+	#end if
+
+
+	#if str($veptools.veptoolsselect) =="vcf2maf"
+	 ln -s $veptools.input_vcf ./input.vcf;
+        perl $__tool_directory__/vcf2maf.pl
+            --input-vcf ./input.vcf
+            --output-maf $output_maf
+            --vep-forks 1
+            --tumor-id $veptools.tumour_id
+            --normal-id $veptools.normal_id
+            --buffer-size $veptools.buffer
+            --vep-path \$CONDA_DEFAULT_ENV/bin/
+            --vep-data \$CONDA_DEFAULT_ENV/vep_cache
+            --ref-fasta $veptools.reference
+            --species $veptools.species;
+
+        #end if
+		 ]]>
+    </command>
+    <inputs>
+	<conditional name="veptools">
+	  <param name="veptoolsselect" type="select" label="vep">
+        	<option value="downloadcache" selected="true">vep-download-cache</option>
+        	<option value="annotate">vep-annotate</option>
+		<option value="vcf2maf">vcf2maf</option>
+      	  </param>
+      	   <when value="downloadcache">
+		<expand macro="list-cache"/>
+	   </when>
+           <when value="annotate">
+		<expand macro="vep-annotate-inputs-macro"/>
+		<expand macro="list-cache-annotate"/>
+	   </when>
+	   <when value="vcf2maf">
+		<expand macro="vcf2maf-inputs-macro"/>
+		<expand macro="list-vcf2maf"/>
+	   </when>
+	</conditional>
+    </inputs>
+    <outputs>
+	<!--vep-download-cache-outputs-->
+	<data format="txt" name="output1" label="cache downloaded">
+		<filter>veptools['veptoolsselect'] == 'downloadcache'</filter>
+	</data>
+	<!--vep-annotate-outputs-->
+	<data format="vcf" name="output2" label="vep-annotated on ${on_string} ">
+		<filter>veptools['veptoolsselect'] == 'annotate'</filter>
+	</data>
+        <data format="html" name="stat" from_work_dir="stat.htm" label="stat on ${on_string}">
+		<filter>veptools['veptoolsselect'] == 'annotate'</filter>
+	</data>
+	<!--vcf2maf-outputs-->
+	<data name="output_maf" format="maf" label="vcf2maf on ${on_string} ">
+		<filter>veptools['veptoolsselect'] == 'vcf2maf'</filter>
+	</data>
+    </outputs>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Failure" />
+    </stdio>
+    <citations>
+    <citation type="doi">10.1186/s13059-016-0974-4</citation>
+    </citations>
+    <help>
+**IMPORTANT**
+        before running vep_annotate or vcf2maf tool for the first time you have to download the cache file using vep_download_cache
+
+	 **what it does**
+
+		- **vep_annotate** determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
+
+		- **vep_download_cache** download the cache file, used by vep v.86.It is a file containing all transcript models, regulatory features and variant data for a species.
+
+		- **vcf2maf** convert vcf in MAF format calling vep_annotate.
+
+    </help>
+</tool>