diff tbvcfreport.xml @ 2:4934c0ac6197 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"

--- a/tbvcfreport.xml	Wed Jul 07 09:22:44 2021 +0000
+++ b/tbvcfreport.xml	Thu Mar 17 07:33:00 2022 +0000
@@ -2,7 +2,7 @@
 <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@">0.1.8</token>
+    <token name="@TOOL_VERSION@">0.1.10</token>
   </macros>
   <requirements>
     <requirement type="package" version="@TOOL_VERSION@">tbvcfreport</requirement>
@@ -64,7 +64,7 @@
     <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" />
+      <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" />
     </section>
   </inputs>
   <outputs>
@@ -78,12 +78,12 @@
     </data>
   </outputs>
   <tests>
-    <test>
+    <test expect_num_outputs="2">
       <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>
+    <test expect_num_outputs="4">
       <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_with_lineage.html" ftype="html" />
@@ -91,6 +91,12 @@
       <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>
+    <test expect_num_outputs="2">
+      <!-- test for bug fixed in 0.1.9 onwards: a gene with no protein product -->
+      <param name="input_vcf" value="vcf_with_no_protein.vcf" ftype="vcf" />
+      <output name="variants_report_html" compare="diff" lines_diff="2" file="vcf_with_no_protein_report.html" ftype="html" />
+      <output name="variants_report_txt" compare="diff" lines_diff="2" file="vcf_with_no_protein_report.txt" ftype="txt" />      
+    </test>
   </tests>
   <help>
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