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comparison tbvcfreport.xml @ 3:42818629ec4c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
author iuc
date Fri, 31 May 2024 20:06:49 +0000
parents 4934c0ac6197
children 9793bc5d741b
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2:4934c0ac6197 3:42818629ec4c
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" profile="23.0" license="AGPL-3.0-or-later">
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@">0.1.10</token> 5 <token name="@TOOL_VERSION@">1.0.0</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">
60 ]]> 60 ]]>
61 </command> 61 </command>
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 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 COMBAT-TB-NeoDB URI" help="For people with their own 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>
100 </tests> 100 </tests>
101 <help> 101 <help>
102 <![CDATA[ 102 <![CDATA[
103 **tbvcfreport - @TOOL_VERSION@** 103 **tbvcfreport - @TOOL_VERSION@**
104 104
105 **tbvcfreport** takes SnpEff annotated M.tuberculosis VCF file(s) and generates an HTML-based report with data from Combat-TB-NeoDB (https://neodb.sanbi.ac.za) 105 **tbvcfreport** takes SnpEff annotated M.tuberculosis VCF file(s) and generates an HTML-based report with data from Combat-TB-NeoDB
106 and links to Combat-TB-eXplorer (https://explorer.sanbi.ac.za/). 106 and links to Combat-TB-eXplorer (https://explorer.sanbi.ac.za/).
107 107
108 **tbvcfreport** will generate an HTML-based Drug Resistance report if provided with a TBProfiler json report. 108 **tbvcfreport** will generate an HTML-based Drug Resistance report if provided with a TBProfiler json report.
109 109
110 Drug resistance predictions are for **Research Purposes Only** and are produced by TBProfiler (https://github.com/jodyphelan/TBProfiler) 110 Drug resistance predictions are for **Research Purposes Only** and are produced by TBProfiler (https://github.com/jodyphelan/TBProfiler)