diff cnv-vcf2json.xml @ 0:c8caf812d33b draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json commit 485fd56c701872217e6d6ccc4321c1f0522ad540

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cnv-vcf2json.xml	Fri Mar 01 07:19:35 2024 +0000
@@ -0,0 +1,31 @@
+<tool id="cnv_vcf2json" name="CNV VCF2JSON" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Converts 1000hg structural variants VCF file to JSON</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="creators"/>
+    <command detect_errors="exit_code"><![CDATA[   
+        #import re
+        ln -s '$input_vcf_file' ./input.vcf &&
+        cnv-vcf2json
+            -i ./input.vcf
+            -o output.json
+    ]]></command>
+    <inputs>
+        <param name="input_vcf_file" type="data" format="vcf" label="CNV VCF file" help="" />
+    </inputs>
+    <outputs>
+        <data name="output_json" format="json" label="${tool.name} on ${on_string}: CNV JSON File" from_work_dir="output.json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_vcf_file" ftype="vcf" value="HG00096.cnv.vcf" />
+            <output name="output_json" file="output.json" />
+        </test>
+    </tests>
+    <help><![CDATA[
+         The tool converts the structural variants VCF file into JSON file as a preprocessing step to import the data into Beacon2 MongoDB protocol
+    ]]></help>
+    <expand macro="citations"/>
+</tool>