# HG changeset patch
# User iuc
# Date 1696958982 0
# Node ID 7d56a813fd24c37865cf55f15afed75079315e18
# Parent  c61bc8bb5f1e963512a7d1a5759a4d3cc0df7d1f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit 34255461a89adf6cdd9e781ac1fe47e8c41227ba

diff -r c61bc8bb5f1e -r 7d56a813fd24 hapog.xml
--- a/hapog.xml	Fri Sep 16 13:48:54 2022 +0000
+++ b/hapog.xml	Tue Oct 10 17:29:42 2023 +0000
@@ -1,7 +1,7 @@
 <tool id="hapog" name="Hapo-G" profile="21.05" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>genome polishing</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.3.3</token>
+        <token name="@TOOL_VERSION@">1.3.6</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
@@ -12,7 +12,10 @@
 --genome '${genome}'
 --output output/
 
---threads \${GALAXY_SLOTS:-1}
+## setting default threads to 2 until
+## https://github.com/institut-de-genomique/HAPO-G/issues/34
+## gets addressed, at least
+--threads \${GALAXY_SLOTS:-2}
 
 #if str( $reads.type ) == "short":
     #for $i in $reads.pe1
@@ -60,8 +63,8 @@
         <param argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Include unpolished sequences in final output" />
     </inputs>
     <outputs>
-        <data format="fasta" name="output" from_work_dir="output/hapog_results/hapog.fasta"/>
-        <data format="tsv" name="changes" from_work_dir="output/hapog_results/hapog.changes"/>
+        <data format="fasta" name="output" label="${tool.name}: polished assembly from ${on_string}" from_work_dir="output/hapog_results/hapog.fasta"/>
+        <data format="tsv" name="changes" label="${tool.name}: report of changes" from_work_dir="output/hapog_results/hapog.changes"/>
     </outputs>
     <tests>
         <test>
diff -r c61bc8bb5f1e -r 7d56a813fd24 test-data/hapog_bam.changes
--- a/test-data/hapog_bam.changes	Fri Sep 16 13:48:54 2022 +0000
+++ b/test-data/hapog_bam.changes	Tue Oct 10 17:29:42 2023 +0000
@@ -1,3 +1,3 @@
 NC_0129201	72	ref=A	read=G	readname=M01368:8:000000000-A3GHV:1:1101:6911:8255	homo	ratio1=1.0000	ratio2=1.0000
-NC_0129201	16525	ref=G	read=A	readname=M01368:8:000000000-A3GHV:1:1104:11928:24197	homo	ratio1=0.9758	ratio2=0.9758
+NC_0129201	16525	ref=G	read=A	readname=M01368:8:000000000-A3GHV:1:1104:11928:24197	homo	ratio1=0.9752	ratio2=0.9752
 
diff -r c61bc8bb5f1e -r 7d56a813fd24 test-data/hapog_short.changes
--- a/test-data/hapog_short.changes	Fri Sep 16 13:48:54 2022 +0000
+++ b/test-data/hapog_short.changes	Tue Oct 10 17:29:42 2023 +0000
@@ -1,3 +1,3 @@
 NC_0129201	72	ref=A	read=G	readname=M01368:8:000000000-A3GHV:1:1101:6911:8255	homo	ratio1=1.0000	ratio2=1.0000
-NC_0129201	16525	ref=G	read=A	readname=M01368:8:000000000-A3GHV:1:1104:11928:24197	homo	ratio1=0.9758	ratio2=0.9758
+NC_0129201	16525	ref=G	read=A	readname=M01368:8:000000000-A3GHV:1:1104:11928:24197	homo	ratio1=0.9752	ratio2=0.9752