Mercurial > repos > iuc > cnv_phenopacket

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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
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61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
iuc
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1 <tool id="cnv_phenopacket" name="CNV Phenopacket" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
iuc
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2 <description>Builds Phenopacket schema for the structural variants metadata from the 1000hg project</description>
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
iuc
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3 <macros>
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
iuc
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4 <import>macros.xml</import>
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
iuc
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5 </macros>
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
iuc
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6 <expand macro="requirements"/>
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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7 <expand macro="creators"/>
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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8 <command detect_errors="exit_code"><![CDATA[
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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9 #import re
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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10 ln -s '$input_tsv_file' ./input.tsv &&
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
iuc
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11 cnv-phenopacket
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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12 -i ./input.tsv
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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13 -o phenopacket.json
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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14 ]]></command>
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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15 <inputs>
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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16 <param name="input_tsv_file" type="data" format="tabular" label="Metadata file" help="" />
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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17 </inputs>
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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18 <outputs>
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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19 <data name="output_json" format="json" label="${tool.name} on ${on_string}: CNV Metadata JSON File" from_work_dir="phenopacket.json" />
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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20 </outputs>
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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21 <tests>
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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22 <test expect_num_outputs="1">
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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23 <param name="input_tsv_file" ftype="tabular" value="igsr-1000-genomes-30x-on-grch38.tsv" />
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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24 <output name="output_json" file="phenopacket.json" />
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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25 </test>
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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26 </tests>
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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27 <help><![CDATA[
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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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
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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29 ]]></help>
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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30 <expand macro="citations"/>
61aad58c7b2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c
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31 </tool>