Mercurial > repos > iuc > cnv_vcf2json

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json commit fc1282ec68b346988203ead860e9b9d6a47e9efb
author iuc
date Sat, 01 Mar 2025 11:47:41 +0000
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9be5490bb681 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json commit 7b5c842d3c006d2afd00aff1ef833f236a45dd3d
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1 <tool id="cnv_vcf2json" name="CNV VCF2JSON" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>Converts the CNVkit structural variants VCF file to JSON</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="creators"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #import re
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10 ln -s '$input_vcf_file' ./input.vcf &&
9be5490bb681 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json commit 7b5c842d3c006d2afd00aff1ef833f236a45dd3d
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11 cnv-vcf2json
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12 ./input.vcf
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13 #if $advanced_settings.assembly
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14 --assembly '$advanced_settings.assembly'
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15 #end if
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16 #if $advanced_settings.analysis
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17 --analysis '$advanced_settings.analysis'
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18 #end if
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19 #if $advanced_settings.individual
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20 --individual '$advanced_settings.individual'
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21 #end if
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22 #if $advanced_settings.sequence
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23 --sequence '$advanced_settings.sequence'
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24 #end if
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25 #if $advanced_settings.reference
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26 --reference '$advanced_settings.reference'
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27 #end if
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28 #if $advanced_settings.fusion
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29 --fusion '$advanced_settings.fusion'
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30 #end if
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31 -o output.json
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32 ]]></command>
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33 <inputs>
1
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34 <param name="input_vcf_file" type="data" format="vcf" label="CNVkit VCF file" help="The file Generated from CNVkit Export" />
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35 <section name="advanced_settings" title="Advanced settings" expanded="false">
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36 <param argument="--assembly" type="text" optional="true" label="Assembly Identifier" help="For example: GRCh37" >
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37 <validator type="regex">^[0-9a-zA-Z_ .-]+$</validator>
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38 </param>
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39 <param argument="--analysis" type="text" optional="true" label="Analysis Identifier" help="" >
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40 <validator type="regex">^[0-9a-zA-Z_,: .-]+$</validator>
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41 </param>
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42 <param argument="--individual" type="text" optional="true" label="Individual Identifier" help="" >
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43 <validator type="regex">^[0-9a-zA-Z_,: .-]+$</validator>
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44 </param>
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45 <param argument="--sequence" type="text" optional="true" label="Variant Sequence" help="" >
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46 <validator type="regex">^[0-9a-zA-Z_,: .-]+$</validator>
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47 </param>
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48 <param argument="--reference" type="text" optional="true" label="Reference Sequence" help="" >
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49 <validator type="regex">^[0-9a-zA-Z_,: .-]+$</validator>
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50 </param>
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51 <param argument="--fusion" type="text" optional="true" label="Fusion Identifier" help="" >
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52 <validator type="regex">^[0-9a-zA-Z_,: .-]+$</validator>
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53 </param>
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54 </section>
0
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55 </inputs>
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56 <outputs>
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57 <data name="output_json" format="json" label="${tool.name} on ${on_string}: CNV JSON File" from_work_dir="output.json" />
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58 </outputs>
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59 <tests>
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60 <test expect_num_outputs="1">
1
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61 <param name="input_vcf_file" ftype="vcf" value="input.vcf" />
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62 <param name="assembly" value="GRCh37" />
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63 <output name="output_json">
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64 <assert_contents>
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65 <has_json_property_with_text property="biosampleId" text="SampleID" />
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66 </assert_contents>
0
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67 </output>
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68 </test>
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69 </tests>
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70 <help><![CDATA[
1
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71 The tool converts the structural variants VCF file generated from the CNVkit export subcommand into JSON file as a preprocessing step to import the data into Beacon2 MongoDB protocol
0
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72 ]]></help>
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73 <expand macro="citations"/>
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74 </tool>