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comparison tbvcfreport.xml @ 2:bda58fe79026 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
author iuc
date Thu, 17 Mar 2022 07:32:28 +0000
parents 46e77cccd665
children
comparison
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1:46e77cccd665 2:bda58fe79026
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="tbvcfreport" name="TB Variant Report" version="@TOOL_VERSION@+galaxy0"> 2 <tool id="tbvcfreport" name="TB Variant Report" version="@TOOL_VERSION@+galaxy0">
3 <description>- generate HTML report from SnpEff annotated M.tb VCF(s)</description> 3 <description>- generate HTML report from SnpEff annotated M.tb VCF(s)</description>
4 <macros> 4 <macros>
5 <token name="@TOOL_VERSION@">0.1.8</token> 5 <token name="@TOOL_VERSION@">0.1.10</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">tbvcfreport</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">tbvcfreport</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"> 10 <command detect_errors="exit_code">
62 <inputs> 62 <inputs>
63 <param name="input_vcf" type="data" format="vcf" label="Input SnpEff annotated M.tuberculosis VCF(s)" /> 63 <param name="input_vcf" type="data" format="vcf" label="Input SnpEff annotated M.tuberculosis VCF(s)" />
64 <param name="tbprofiler_json" type="data" format="json" optional="true" label="TBProfiler Drug Resistance Report (Optional)" help="--tbprofiler-report" /> 64 <param name="tbprofiler_json" type="data" format="json" optional="true" label="TBProfiler Drug Resistance Report (Optional)" help="--tbprofiler-report" />
65 <param name="filter_udi" argument="--filter-udi" type="boolean" truevalue="--filter-udi" falsevalue="--no-filter-udi" checked="true" label="Filter UPSTREAM, DOWNSTREAM and INTERGENIC variants" /> 65 <param name="filter_udi" argument="--filter-udi" type="boolean" truevalue="--filter-udi" falsevalue="--no-filter-udi" checked="true" label="Filter UPSTREAM, DOWNSTREAM and INTERGENIC variants" />
66 <section name="adv" title="Advanced options" expanded="false"> 66 <section name="adv" title="Advanced options" expanded="false">
67 <param name="database_uri" type="text" optional="true" value="neodb.sanbi.ac.za" label="Specify on-premise COMBAT-TB-NeoDB URI" help="For people with an on-premise deployment of COMBAT-TB-NeoDB" /> 67 <param name="database_uri" type="text" optional="true" value="neodb.sanbi.ac.za" label="Specify COMBAT-TB-NeoDB URI" help="For people with their own deployment of COMBAT-TB-NeoDB" />
68 </section> 68 </section>
69 </inputs> 69 </inputs>
70 <outputs> 70 <outputs>
71 <data name="variants_report_html" format="html" label="${tool.name} variants report (html) on ${on_string}" /> 71 <data name="variants_report_html" format="html" label="${tool.name} variants report (html) on ${on_string}" />
72 <data name="variants_report_txt" format="txt" label="${tool.name} variants report (text) on ${on_string}" /> 72 <data name="variants_report_txt" format="txt" label="${tool.name} variants report (text) on ${on_string}" />
76 <data name="drug_resistance_report_txt" format="txt" label="${tool.name} drug resistance report (text) on ${on_string}"> 76 <data name="drug_resistance_report_txt" format="txt" label="${tool.name} drug resistance report (text) on ${on_string}">
77 <filter>tbprofiler_json</filter> 77 <filter>tbprofiler_json</filter>
78 </data> 78 </data>
79 </outputs> 79 </outputs>
80 <tests> 80 <tests>
81 <test> 81 <test expect_num_outputs="2">
82 <param name="input_vcf" value="rif_resistant.vcf" ftype="vcf" /> 82 <param name="input_vcf" value="rif_resistant.vcf" ftype="vcf" />
83 <output name="variants_report_html" compare="diff" lines_diff="2" file="rif_resistant_variants_report.html" ftype="html" /> 83 <output name="variants_report_html" compare="diff" lines_diff="2" file="rif_resistant_variants_report.html" ftype="html" />
84 <output name="variants_report_txt" compare="diff" lines_diff="2" file="rif_resistant_variants_report.txt" ftype="txt" /> 84 <output name="variants_report_txt" compare="diff" lines_diff="2" file="rif_resistant_variants_report.txt" ftype="txt" />
85 </test> 85 </test>
86 <test> 86 <test expect_num_outputs="4">
87 <param name="input_vcf" value="rif_resistant.vcf" ftype="vcf" /> 87 <param name="input_vcf" value="rif_resistant.vcf" ftype="vcf" />
88 <param name="tbprofiler_json" value="rif_resistant.results.json" ftype="json" /> 88 <param name="tbprofiler_json" value="rif_resistant.results.json" ftype="json" />
89 <output name="variants_report_html" compare="diff" lines_diff="2" file="rif_resistant_variants_report_with_lineage.html" ftype="html" /> 89 <output name="variants_report_html" compare="diff" lines_diff="2" file="rif_resistant_variants_report_with_lineage.html" ftype="html" />
90 <output name="variants_report_txt" compare="diff" lines_diff="2" file="rif_resistant_variants_report_with_lineage.txt" ftype="txt" /> 90 <output name="variants_report_txt" compare="diff" lines_diff="2" file="rif_resistant_variants_report_with_lineage.txt" ftype="txt" />
91 <output name="drug_resistance_report_html" file="rif_resistant_drug_resistance_report.html" lines_diff="2" ftype="html" /> 91 <output name="drug_resistance_report_html" file="rif_resistant_drug_resistance_report.html" lines_diff="2" ftype="html" />
92 <output name="drug_resistance_report_txt" compare="diff" lines_diff="2" file="rif_resistant_drug_resistance_report.txt" ftype="txt" /> 92 <output name="drug_resistance_report_txt" compare="diff" lines_diff="2" file="rif_resistant_drug_resistance_report.txt" ftype="txt" />
93 </test>
94 <test expect_num_outputs="2">
95 <!-- test for bug fixed in 0.1.9 onwards: a gene with no protein product -->
96 <param name="input_vcf" value="vcf_with_no_protein.vcf" ftype="vcf" />
97 <output name="variants_report_html" compare="diff" lines_diff="2" file="vcf_with_no_protein_report.html" ftype="html" />
98 <output name="variants_report_txt" compare="diff" lines_diff="2" file="vcf_with_no_protein_report.txt" ftype="txt" />
93 </test> 99 </test>
94 </tests> 100 </tests>
95 <help> 101 <help>
96 <![CDATA[ 102 <![CDATA[
97 **tbvcfreport - @TOOL_VERSION@** 103 **tbvcfreport - @TOOL_VERSION@**