diff cnv-phenopacket.xml @ 0:61aad58c7b2d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cnv-phenopacket.xml	Fri Mar 01 19:04:08 2024 +0000
@@ -0,0 +1,31 @@
+<tool id="cnv_phenopacket" name="CNV Phenopacket" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>Builds Phenopacket schema for the structural variants metadata from the 1000hg project</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="creators"/>
+    <command detect_errors="exit_code"><![CDATA[   
+        #import re
+        ln -s '$input_tsv_file' ./input.tsv &&
+        cnv-phenopacket
+            -i ./input.tsv
+            -o phenopacket.json
+    ]]></command>
+    <inputs>
+        <param name="input_tsv_file" type="data" format="tabular" label="Metadata file" help="" />
+    </inputs>
+    <outputs>
+        <data name="output_json" format="json" label="${tool.name} on ${on_string}: CNV Metadata JSON File" from_work_dir="phenopacket.json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_tsv_file" ftype="tabular" value="igsr-1000-genomes-30x-on-grch38.tsv" />
+            <output name="output_json" file="phenopacket.json" />
+        </test>
+    </tests>
+    <help><![CDATA[
+         The tool extracts the metadata for the variants from the TSV file and and converts them into JSON file as a preprocessing step to import the data into Beacon2 MongoDB protocol
+    ]]></help>
+    <expand macro="citations"/>
+</tool>