Mercurial > repos > iuc > cnv_vcf2json

annotate cnv-vcf2json.xml @ 0:c8caf812d33b draft

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