comparison cnv-vcf2json.xml @ 0:c8caf812d33b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json commit 485fd56c701872217e6d6ccc4321c1f0522ad540
author iuc
date Fri, 01 Mar 2024 07:19:35 +0000
parents
children 7d2d2e3b9891
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-1:000000000000 0:c8caf812d33b
1 <tool id="cnv_vcf2json" name="CNV VCF2JSON" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Converts 1000hg structural variants VCF file to JSON</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="creators"/>
8 <command detect_errors="exit_code"><![CDATA[
9 #import re
10 ln -s '$input_vcf_file' ./input.vcf &&
11 cnv-vcf2json
12 -i ./input.vcf
13 -o output.json
14 ]]></command>
15 <inputs>
16 <param name="input_vcf_file" type="data" format="vcf" label="CNV VCF file" help="" />
17 </inputs>
18 <outputs>
19 <data name="output_json" format="json" label="${tool.name} on ${on_string}: CNV JSON File" from_work_dir="output.json" />
20 </outputs>
21 <tests>
22 <test expect_num_outputs="1">
23 <param name="input_vcf_file" ftype="vcf" value="HG00096.cnv.vcf" />
24 <output name="output_json" file="output.json" />
25 </test>
26 </tests>
27 <help><![CDATA[
28 The tool converts the structural variants VCF file into JSON file as a preprocessing step to import the data into Beacon2 MongoDB protocol
29 ]]></help>
30 <expand macro="citations"/>
31 </tool>