# HG changeset patch
# User iuc
# Date 1621703377 0
# Node ID 424dcb6f76d34408ba3d9fa6c970e55a94fa8a42
# Parent  b444a6bda4a448757987db77c38a704baf020517
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 9fa7ac6aaaf97db392a1bf93741a6d271b619ed3"

diff -r b444a6bda4a4 -r 424dcb6f76d3 macros.xml
--- a/macros.xml	Wed Jan 06 14:41:46 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-<macros>
-    <token name="@TOOL_VERSION@">2.8.14</token>
-</macros>
diff -r b444a6bda4a4 -r 424dcb6f76d3 tb_profiler_profile.xml
--- a/tb_profiler_profile.xml	Wed Jan 06 14:41:46 2021 +0000
+++ b/tb_profiler_profile.xml	Sat May 22 17:09:37 2021 +0000
@@ -1,7 +1,7 @@
-<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy1">
+<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy1" profile="21.01">
     <description>Infer strain types and drug resistance markers from sequences</description>
     <macros>
-        <import>macros.xml</import>
+        <token name="@TOOL_VERSION@">3.0.4</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement>
@@ -91,7 +91,7 @@
             </when>
         </conditional>
         <param name="output_format" label="Output format" type="select">
-            <option value="txt">Text</option>
+            <option value="txt" selected="true">Text</option>
             <option value="pdf">PDF</option>
         </param>
         <conditional name="advanced">
@@ -128,7 +128,7 @@
 
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="4">
             <param name="input_select" value="single_fastq"/>
             <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" />
             <param name="output_format" value="txt" />
@@ -136,14 +136,14 @@
             <param name="options" value="no" />
             <output name="output_txt">
                 <assert_contents>
-                    <has_line line="Drug-resistance: Drug-resistant" />
+                    <has_line line="Drug-resistance: Pre-MDR" />
                     <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" />
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input_select" value="bam"/>
             <param name="bam_input" ftype="bam" value="rif_resistant.bam" />
             <param name="output_format" value="txt" />
@@ -151,14 +151,14 @@
             <param name="options" value="no" />
             <output name="output_txt">
                 <assert_contents>
-                    <has_line line="Drug-resistance: Drug-resistant" />
+                    <has_line line="Drug-resistance: Pre-MDR" />
                     <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" />
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="4">
             <param name="input_select" value="single_fastq"/>
             <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" />
             <param name="output_format" value="txt" />
@@ -169,7 +169,7 @@
             <param name="min_allele_freq_reporting" value="0.33" />
             <output name="output_txt">
                 <assert_contents>
-                    <has_line line="Drug-resistance: Drug-resistant" />
+                    <has_line line="Drug-resistance: Pre-MDR" />
                     <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" />
@@ -181,19 +181,15 @@
 Summary
 =======
 
-The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using GATK. These variants are then compared to a drug-resistance database. We also predict the number of reads supporting drug resistance variants as an insight into hetero-resistance (not applicable for minION data).
+The pipeline aligns reads to the H37Rv reference using BWA, bowtie2 or minimap2 and then calls variants 
+(using bcftools, GATK4 or freebayes). These variants are then compared to a drug-resistance database. 
+TB-Profiler also predicts the number of reads supporting drug resistance variants as an insight into
+hetero-resistance (not applicable for MinION data).
 
 Produces a JSON output file by default.
 
     ]]>    </help>
     <citations>
-        <citation type="bibtex">
-@UNPUBLISHED{Phelan2016,
-    author = {Phelan, Jody},
-    title = {TBProfiler},
-    year = {2016},
-    url = {https://github.com/jodyphelan/TBProfiler},
-}
-        </citation>
+        <citation type="doi">10.1186/s13073-019-0650-x</citation>
     </citations>
 </tool>