# HG changeset patch
# User iuc
# Date 1672500969 0
# Node ID 45083d070fb89e1fc96eda772f63b8fc6ffb4859
# Parent  ac8250086ac3d54f718c84414246a4e0c0a37451
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 9dd4c8aca212218a9e8f8a49013c255696191b0f

diff -r ac8250086ac3 -r 45083d070fb8 tb_profiler_profile.xml
--- a/tb_profiler_profile.xml	Wed Mar 16 09:15:44 2022 +0000
+++ b/tb_profiler_profile.xml	Sat Dec 31 15:36:09 2022 +0000
@@ -1,7 +1,7 @@
 <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0" profile="20.09">
     <description>Infer strain types and drug resistance markers from sequences</description>
     <macros>
-        <token name="@TOOL_VERSION@">4.1.1</token>
+        <token name="@TOOL_VERSION@">4.4.0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement>
@@ -67,6 +67,7 @@
         <param name="platform" type="select" label="Platform">
             <option value="illumina" selected="true">Illumina</option>
             <option value="nanopore">Nanopore</option>
+            <option value="pacbio">PacBio</option>
         </param>
         <conditional name="fastq_or_bam">
             <param name="input_select" type="select" label="Input File Type">
@@ -144,9 +145,9 @@
             <output name="output_txt">
                 <assert_contents>
                     <has_line line="Drug-resistance: RR-TB" />
-                    <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
+                    <has_line line="lineage2.2.2&#009;1.000&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
                     <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
-                    <has_line line="761110&#009;Rv0667&#009;rpoB&#009;p.Asp435Val&#009;1.000&#009;rifampicin" />
+                    <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" />
                 </assert_contents>
             </output>
         </test>
@@ -159,9 +160,9 @@
             <output name="output_txt">
                 <assert_contents>
                     <has_line line="Drug-resistance: RR-TB" />
-                    <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
+                    <has_line line="lineage2.2.2&#009;1.000&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
                     <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
-                    <has_line line="761110&#009;Rv0667&#009;rpoB&#009;p.Asp435Val&#009;1.000&#009;rifampicin" />
+                    <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" />
                 </assert_contents>
             </output>
         </test>
@@ -171,15 +172,14 @@
             <param name="output_format" value="txt" />
             <param name="platform" value="illumina" />
             <param name="options" value="yes" />
-            <param name="call_whole_genome" value="true" />
             <param name="min_allele_freq" value="0.25" />
             <param name="min_allele_freq_reporting" value="0.33" />
             <output name="output_txt">
                 <assert_contents>
                     <has_line line="Drug-resistance: RR-TB" />
-                    <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
+                    <has_line line="lineage2.2.2&#009;1.000&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
                     <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
-                    <has_line line="761110&#009;Rv0667&#009;rpoB&#009;p.Asp435Val&#009;1.000&#009;rifampicin" />
+                    <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" />
                 </assert_contents>
             </output>
         </test>