# HG changeset patch
# User iuc
# Date 1647422144 0
# Node ID ac8250086ac3d54f718c84414246a4e0c0a37451
# Parent  809dfc93d593608d82a2208303cc9463cd0c90f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 7598f8402d6adaab0e7c9a3cd426914f700be336"

diff -r 809dfc93d593 -r ac8250086ac3 tb_profiler_profile.xml
--- a/tb_profiler_profile.xml	Mon Sep 06 17:20:56 2021 +0000
+++ b/tb_profiler_profile.xml	Wed Mar 16 09:15:44 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@">3.0.8</token>
+        <token name="@TOOL_VERSION@">4.1.1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement>
@@ -27,9 +27,7 @@
         #end if
 
         tb-profiler profile
-            
             --platform '${platform.value}'
-
         #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
             -1 fastq_r1.'$r1_ext'
         #end if
@@ -42,6 +40,7 @@
             --threads "\${GALAXY_SLOTS:-1}"
         #if $advanced.options == 'yes'
             --mapper '${advanced.mapper}'
+            --caller '${advanced.caller}'
             --min_depth '${advanced.min_depth}'
             --af '${advanced.min_allele_freq}'
             --reporting_af '${advanced.min_allele_freq_reporting}'
@@ -102,10 +101,18 @@
             <when value="no">
             </when>
             <when value="yes">
-                <param name="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)">
+                <param argument="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)">
                     <option value="bwa" selected="true">bwa</option>
                     <option value="minimap2">minimap2</option>
                     <option value="bowtie2">bowtie2</option>
+                    <option value="bwa-mem2">bwa-mem2</option>
+                </param>
+                <param argument="caller" label="Variant caller" help="Variant calling tool to use" type="select">
+                    <option value="freebayes" selected="true">freebayes</option>
+                    <option value="bcftools">bcftools</option>
+                    <option value="gatk">gatk</option>
+                    <option value="pilon">pilon</option>
+                    <option value="lofreq">lofreq</option>
                 </param>
                 <param name="min_depth" label="Min Depth" type="integer" value="10" help="Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing (default: 10)"/>
                 <param name="min_allele_freq" argument="--af" type="float" value="0.1" label="Minimum allele frequency to call variants" help=" Minimum allele frequency to call variants (default: 0.1)" />
@@ -136,10 +143,10 @@
             <param name="options" value="no" />
             <output name="output_txt">
                 <assert_contents>
-                    <has_line line="Drug-resistance: Pre-MDR" />
+                    <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="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
-                    <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" />
+                    <has_line line="761110&#009;Rv0667&#009;rpoB&#009;p.Asp435Val&#009;1.000&#009;rifampicin" />
                 </assert_contents>
             </output>
         </test>
@@ -151,10 +158,10 @@
             <param name="options" value="no" />
             <output name="output_txt">
                 <assert_contents>
-                    <has_line line="Drug-resistance: Pre-MDR" />
+                    <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="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
-                    <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" />
+                    <has_line line="761110&#009;Rv0667&#009;rpoB&#009;p.Asp435Val&#009;1.000&#009;rifampicin" />
                 </assert_contents>
             </output>
         </test>
@@ -169,10 +176,10 @@
             <param name="min_allele_freq_reporting" value="0.33" />
             <output name="output_txt">
                 <assert_contents>
-                    <has_line line="Drug-resistance: Pre-MDR" />
+                    <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="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
-                    <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" />
+                    <has_line line="761110&#009;Rv0667&#009;rpoB&#009;p.Asp435Val&#009;1.000&#009;rifampicin" />
                 </assert_contents>
             </output>
         </test>