--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcf2bff.xml	Sun Oct 01 16:29:00 2023 +0000
@@ -0,0 +1,50 @@
+<tool id="beacon2_vcf2bff" name="Beacon2 VCF2BFF" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>converting annotated VCF files to Beacon v2 format</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <expand macro="creators"/>
+    <command detect_errors="exit_code"><![CDATA[   
+        ln -s '$input' ./sample.vcf.gz &&
+        vcf2bff.pl
+            --input ./sample.vcf.gz
+            --format '$format'
+            --project-dir ./
+            --dataset-id '$dataset_id'
+            --genome '$genome'
+        && gunzip ./genomicVariationsVcf.json.gz
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="tabular.gz" label="Annotated vcf file" help="The output genomic variations VCF file of bcftools, snpeff, snpsift" />
+        <param argument="--format" type="select" label="Output format" help="">
+            <option value="bff" selected="True">BFF</option>
+            <option value="hash">hash</option>
+            <option value="json">json</option>
+        </param>
+        <param argument="--dataset-id" type="text" label="Dataset ID" value="" help="Give an ID for the created genomicVariations dataset" />
+        <param argument="--genome" type="text" label="Reference genome" value="" help="Select the reference genome used the annotate the data to create the genomicVariations dataset examples for reference genomes are hs37, hg37 and hg38" />
+    </inputs>
+    <outputs>
+        <data name="genomicVariationsVcf" format="json" label="${tool.name} on ${on_string}: genomicVariationsVcf file" from_work_dir="genomicVariationsVcf.json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" ftype="tabular.gz" value="test.vcf.gz" />
+            <param name="format" value="bff"/>
+            <param name="dataset_id" value="beacon"/>
+            <param name="genome" value="hg19"/>
+            <output name="genomicVariationsVcf" file="genomicVariationsVcf.json" ftype="json" compare="sim_size">
+                <assert_contents><has_size value="730000" delta="90000" /></assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+          The tool Creates genomicVariations file from annotated genomic variations VCF file. The VCF file is annotated by using the
+          workflow of those tools bcftools -> snpeff -> snpsift.
+          The tool converts the annotated VCF file into genomicVariations entry type and serializes it as a JSON file also called Beacon Friendly Format (BFF).
+          The generated file will be ready to be stored on the MongoDB instance as MongoDB works directly with JSON files.
+    ]]></help>
+    <expand macro="citations" />
+</tool>