Mercurial > repos > iuc > cnv_phenopacket
comparison 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
| author | iuc |
|---|---|
| date | Fri, 01 Mar 2024 19:04:08 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:61aad58c7b2d |
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| 1 <tool id="cnv_phenopacket" name="CNV Phenopacket" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | |
| 2 <description>Builds Phenopacket schema for the structural variants metadata from the 1000hg project</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 '$input_tsv_file' ./input.tsv && | |
| 11 cnv-phenopacket | |
| 12 -i ./input.tsv | |
| 13 -o phenopacket.json | |
| 14 ]]></command> | |
| 15 <inputs> | |
| 16 <param name="input_tsv_file" type="data" format="tabular" label="Metadata file" help="" /> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data name="output_json" format="json" label="${tool.name} on ${on_string}: CNV Metadata JSON File" from_work_dir="phenopacket.json" /> | |
| 20 </outputs> | |
| 21 <tests> | |
| 22 <test expect_num_outputs="1"> | |
| 23 <param name="input_tsv_file" ftype="tabular" value="igsr-1000-genomes-30x-on-grch38.tsv" /> | |
| 24 <output name="output_json" file="phenopacket.json" /> | |
| 25 </test> | |
| 26 </tests> | |
| 27 <help><![CDATA[ | |
| 28 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 | |
| 29 ]]></help> | |
| 30 <expand macro="citations"/> | |
| 31 </tool> |