--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tbvcfreport.xml	Thu Aug 29 08:18:59 2019 -0400
@@ -0,0 +1,143 @@
+<?xml version="1.0" ?>
+<tool id="tbvcfreport" name="TB Variant Report" version="@TOOL_VERSION@+galaxy0">
+  <description>- generate HTML report from SnpEff annotated M.tb VCF(s)</description>
+  <macros>
+    <token name="@TOOL_VERSION@">0.1.7</token>
+  </macros>
+  <requirements>
+    <requirement type="package" version="@TOOL_VERSION@">tbvcfreport</requirement>
+  </requirements>
+  <command detect_errors="exit_code">
+    <![CDATA[
+    #if $adv.database_uri
+        export DATABASE_URI='${adv.database_uri}' &&
+    #end if
+    
+    #if not '.vcf' in str($input_vcf.element_identifier)
+        #set $input_vcf_filename = str($input_vcf.element_identifier).replace(' ', '') + '.vcf'
+    #else
+        #set $input_vcf_filename = str($input_vcf.element_identifier).replace(' ', '')
+    #end if
+
+    ln -s '${input_vcf}' '${input_vcf_filename}' &&
+    
+    #set vcf_name = os.path.splitext(os.path.basename($input_vcf_filename))[0]
+    
+    #if $tbprofiler_json
+        #if not '.json' in str($tbprofiler_json.element_identifier)
+          #set $tbprofiler_report = str($tbprofiler_json.element_identifier).replace(' ', '') + '.json'
+        #else
+            #set $tbprofiler_report = str($tbprofiler_json.element_identifier).replace(' ', '')
+        #end if
+        ln -s '${tbprofiler_json}' '${tbprofiler_report}' &&
+    #end if
+
+    tbvcfreport generate
+
+    $filter_udi
+    
+    #if $tbprofiler_json
+        --tbprofiler-report '${tbprofiler_report}'
+    #end if
+    
+    '${input_vcf_filename}' &&
+
+    #set variants_report = str(vcf_name) + '_variants_report'
+    #set html_variants_report = variants_report + '.html'
+    #set txt_variants_report = variants_report + '.txt'
+
+    mv '${html_variants_report}' '$variants_report_html' &&
+    mv '${txt_variants_report}' '$variants_report_txt'
+
+    #if $tbprofiler_json
+        #set drug_resistance_report = str(vcf_name) + '_drug_resistance_report'
+        #set html_drug_resistance_report = drug_resistance_report + '.html'
+        #set txt_drug_resistance_report = drug_resistance_report + '.txt'
+        
+        && mv '${html_drug_resistance_report}' '$drug_resistance_report_html'
+        && mv '${txt_drug_resistance_report}' '$drug_resistance_report_txt'
+    #end if
+    ]]>
+  </command>
+  <inputs>
+    <param name="input_vcf" type="data" format="vcf" label="Input SnpEff annotated M.tuberculosis VCF(s)" />
+    <param name="tbprofiler_json" type="data" format="json" optional="true" label="TBProfiler Drug Resistance Report (Optional)" help="--tbprofiler-report" />
+    <param name="filter_udi" argument="--filter-udi" type="boolean" truevalue="--filter-udi" falsevalue="--no-filter-udi" checked="true" label="Filter UPSTREAM, DOWNSTREAM and INTERGENIC variants" />
+    <section name="adv" title="Advanced options" expanded="false">
+      <param name="database_uri" type="text" optional="true" value="neodb.sanbi.ac.za" label="Specify on-premise COMBAT-TB-NeoDB URI" help="For people with an on-premise deployment of COMBAT-TB-NeoDB" />
+    </section>
+  </inputs>
+  <outputs>
+    <data name="variants_report_html" format="html" label="${tool.name} variants report (html) on ${on_string}" />
+    <data name="variants_report_txt" format="txt" label="${tool.name} variants report (text) on ${on_string}" />
+    <data name="drug_resistance_report_html" format="html" label="${tool.name} drug resistance report (html) on ${on_string}">
+      <filter>tbprofiler_json</filter>
+    </data>
+    <data name="drug_resistance_report_txt" format="txt" label="${tool.name} drug resistance report (text) on ${on_string}">
+      <filter>tbprofiler_json</filter>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_vcf" value="rif_resistant.vcf" ftype="vcf" />
+      <output name="variants_report_html" compare="diff" lines_diff="2" file="rif_resistant_variants_report.html" ftype="html" />
+      <output name="variants_report_txt" compare="diff" lines_diff="2" file="rif_resistant_variants_report.txt" ftype="txt" />
+    </test>
+    <test>
+      <param name="input_vcf" value="rif_resistant.vcf" ftype="vcf" />
+      <param name="tbprofiler_json" value="rif_resistant.results.json" ftype="json" />
+      <output name="variants_report_html" compare="diff" lines_diff="2" file="rif_resistant_variants_report.html" ftype="html" />
+      <output name="variants_report_txt" compare="diff" lines_diff="2" file="rif_resistant_variants_report.txt" ftype="txt" />
+      <output name="drug_resistance_report_html" file="rif_resistant_drug_resistance_report.html" lines_diff="2" ftype="html" />
+      <output name="drug_resistance_report_txt" compare="diff" lines_diff="2" file="rif_resistant_drug_resistance_report.txt" ftype="txt" />
+    </test>
+  </tests>
+  <help>
+    <![CDATA[
+    **tbvcfreport - @TOOL_VERSION@**
+
+    **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) 
+    and links to Combat-TB-eXplorer (https://explorer.sanbi.ac.za/).
+
+    **tbvcfreport** will generate an HTML-based Drug Resistance report if provided with a TBProfiler json report.
+    
+    Drug resistance predictions are for **Research Purposes Only** and are produced by TBProfiler (https://github.com/jodyphelan/TBProfiler)
+    
+    **Inputs**
+
+        - SnpEff annotated M.tuberculosis VCF file(s) - vcf - **required**
+        
+        - TBProfiler Drug Resistance JSON Report - json - **optional**
+
+    **Outputs**
+
+        - Variant Report in HTML and TXT format
+        
+        - Drug Resistance Report in HTML and TXT format if provided with a TBProfiler json report
+          
+        
+    **Advanced options**:
+
+        - database_uri - String - Use an on-premise COMBAT-TB-NeoDB (default 'neodb.sanbi.ac.za') - **optional**
+
+    **Further information**
+    
+    For more on the **COMBAT-TB Project**, see https://combattb.org.
+
+    For more on **tbvcfreport**, see https://github.com/COMBAT-TB/tbvcfreport.
+    
+    For more on **COMBAT-TB-NeoDB**, see https://github.com/COMBAT-TB/combat-tb-neodb.
+    ]]>
+  </help>
+  <citations>
+    <citation type="bibtex">
+@misc{githubtbvcfreport,
+  author = {COMBAT-TB},
+  year = {2019},
+  title = {tbvcfreport},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/COMBAT-TB/tbvcfreport},
+}</citation>
+  </citations>
+</tool>