# HG changeset patch
# User iuc
# Date 1705592285 0
# Node ID 1d4bd12f01cf7e6a015590e66b05d59a985ed223
# Parent  978ae4147c29edcb2db72ce1ebf2c57cd0404f9c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857

diff -r 978ae4147c29 -r 1d4bd12f01cf est-abundance.xml
--- a/est-abundance.xml	Mon May 22 19:24:46 2023 +0000
+++ b/est-abundance.xml	Thu Jan 18 15:38:05 2024 +0000
@@ -33,6 +33,8 @@
             </options>
         </param>
         <param name="level" type="select" label="Level" help="Level to push all reads to">
+            <option value="S2">Subspecies 2</option>
+            <option value="S1">Subspecies 1</option>
             <option value="S" selected="true">Species</option>
             <option value="G">Genus</option>
             <option value="F">Family</option>
@@ -74,6 +76,20 @@
             <output name="kraken_report" file="NC_011750.1_simulated_kraken_style_bracken_report.txt" ftype="tabular"/>
             <output name="logfile" file="test2.log" lines_diff="8"/>
         </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/>
+            <param name="level" value="S1"/>
+            <param name="kmer_distr" value="test_entry"/>
+            <param name="logfile_output" value="False"/>
+            <output name="report" file="NC_003198.1_simulated_bracken_report_S1.txt" ftype="tabular"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/>
+            <param name="level" value="S2"/>
+            <param name="kmer_distr" value="test_entry"/>
+            <param name="logfile_output" value="False"/>
+            <output name="report" file="NC_003198.1_simulated_bracken_report_S2.txt" ftype="tabular"/>
+        </test>
     </tests>
     <help>
     <![CDATA[
diff -r 978ae4147c29 -r 1d4bd12f01cf macros.xml
--- a/macros.xml	Mon May 22 19:24:46 2023 +0000
+++ b/macros.xml	Thu Jan 18 15:38:05 2024 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.8</token>
+    <token name="@TOOL_VERSION@">2.9</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="requirements">
diff -r 978ae4147c29 -r 1d4bd12f01cf test-data/NC_003198.1_simulated_bracken_report_S1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_003198.1_simulated_bracken_report_S1.txt	Thu Jan 18 15:38:05 2024 +0000
@@ -0,0 +1,2 @@
+name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads
+Salmonella enterica subsp. enterica	59201	S1	40	2	42	1.00000
diff -r 978ae4147c29 -r 1d4bd12f01cf test-data/NC_003198.1_simulated_bracken_report_S2.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_003198.1_simulated_bracken_report_S2.txt	Thu Jan 18 15:38:05 2024 +0000
@@ -0,0 +1,2 @@
+name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads
+Salmonella enterica subsp. enterica serovar Typhi	90370	S2	40	2	42	1.00000
diff -r 978ae4147c29 -r 1d4bd12f01cf test-data/test2.log
--- a/test-data/test2.log	Mon May 22 19:24:46 2023 +0000
+++ b/test-data/test2.log	Thu Jan 18 15:38:05 2024 +0000
@@ -1,5 +1,5 @@
-PROGRAM START TIME: 08-05-2022 14:41:48
-BRACKEN SUMMARY (Kraken report: /tmp/tmpy56dgetr/files/f/5/4/dataset_f5412c50-3888-4466-b041-32814cdda47c.dat)
+PROGRAM START TIME: 01-18-2024 14:06:58
+BRACKEN SUMMARY (Kraken report: /tmp/tmp49rzn0wx/files/f/a/a/dataset_faa2d0a2-78f4-4cc2-b304-c8202c4ffb77.dat)
     >>> Threshold: 10 
     >>> Number of species in sample: 1 
 	  >> Number of species with reads > threshold: 1 
@@ -10,5 +10,5 @@
 	  >> Reads distributed: 1
 	  >> Reads not distributed (eg. no species above threshold): 0
 	  >> Unclassified reads: 2
-BRACKEN OUTPUT PRODUCED: /tmp/tmpy56dgetr/job_working_directory/000/4/outputs/galaxy_dataset_e099cc44-07e6-4507-b11f-137722113078.dat
-PROGRAM END TIME: 08-05-2022 14:41:48
+BRACKEN OUTPUT PRODUCED: /tmp/tmp49rzn0wx/job_working_directory/000/4/outputs/galaxy_dataset_27bf8d97-38f4-489a-a61b-6b567bbc8761.dat
+PROGRAM END TIME: 01-18-2024 14:06:58