# HG changeset patch
# User iuc
# Date 1712309976 0
# Node ID 5287036a797a1b36e07aff90eac11a3125bfe195
# Parent  ee0d6e789958203833e3f2d31bbef1a57e206925
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog commit 8e54473840ee1238da9cb8a77cf136f00b40e4e7

diff -r ee0d6e789958 -r 5287036a797a hapog.xml
--- a/hapog.xml	Sun Jan 28 23:46:07 2024 +0000
+++ b/hapog.xml	Fri Apr 05 09:39:36 2024 +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@">1.3.7</token>
+        <token name="@TOOL_VERSION@">1.3.8</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <xrefs>
@@ -65,7 +65,7 @@
                 <param name="bam" type="data" format="bam" label="Pre-aligned reads"/>
             </when>
         </conditional>
-        <param argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Include unpolished sequences in final output" />
+        <param argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Include unpolished sequences in final output"/>
     </inputs>
     <outputs>
         <data format="fasta" name="output" label="${tool.name}: polished assembly from ${on_string}" from_work_dir="output/hapog_results/hapog.fasta"/>
@@ -73,51 +73,51 @@
     </outputs>
     <tests>
         <test>
-            <param name="genome" value="genome.fa" />
+            <param name="genome" value="genome.fa"/>
             <conditional name="reads">
-                <param name="type" value="short" />
-                <param name="pe1" value="fastq1.fq" />
-                <param name="pe2" value="fastq2.fq" />
+                <param name="type" value="short"/>
+                <param name="pe1" value="fastq1.fq"/>
+                <param name="pe2" value="fastq2.fq"/>
             </conditional>
-            <output name="output" file="hapog_short.fasta" />
-            <output name="changes" file="hapog_short.changes" />
+            <output name="output" file="hapog_short.fasta"/>
+            <output name="changes" file="hapog_short.changes"/>
         </test>
         <test>
-            <param name="genome" value="genome.fa" />
+            <param name="genome" value="genome.fa"/>
             <conditional name="reads">
-                <param name="type" value="short" />
-                <param name="pe1" value="fastq1.fq.gz" />
-                <param name="pe2" value="fastq2.fq.gz" />
+                <param name="type" value="short"/>
+                <param name="pe1" value="fastq1.fq.gz"/>
+                <param name="pe2" value="fastq2.fq.gz"/>
             </conditional>
             <output name="output" file="hapog_short.fasta"/>
-            <output name="changes" file="hapog_short.changes" />
+            <output name="changes" file="hapog_short.changes"/>
         </test>
         <test>
-            <param name="genome" value="genome.fa" />
+            <param name="genome" value="genome.fa"/>
             <conditional name="reads">
-                <param name="type" value="long" />
-                <param name="single" value="fastq1.fq" />
+                <param name="type" value="long"/>
+                <param name="single" value="fastq1.fq"/>
             </conditional>
-            <output name="output" file="hapog_long.fasta" />
-            <output name="changes" file="hapog_long.changes" />
+            <output name="output" file="hapog_long.fasta"/>
+            <output name="changes" file="hapog_long.changes"/>
         </test>
         <test>
-            <param name="genome" value="genome.fa" />
+            <param name="genome" value="genome.fa"/>
             <conditional name="reads">
-                <param name="type" value="long" />
-                <param name="single" value="fastq1.fq.gz" />
+                <param name="type" value="long"/>
+                <param name="single" value="fastq1.fq.gz"/>
             </conditional>
             <output name="output" file="hapog_long.fasta"/>
-            <output name="changes" file="hapog_long.changes" />
+            <output name="changes" file="hapog_long.changes"/>
         </test>
         <test>
-            <param name="genome" value="genome.fa" />
+            <param name="genome" value="genome.fa"/>
             <conditional name="reads">
-                <param name="type" value="bam" />
-                <param name="bam" value="input.bam" />
+                <param name="type" value="bam"/>
+                <param name="bam" value="input.bam"/>
             </conditional>
             <output name="output" file="hapog_bam.fasta"/>
-            <output name="changes" file="hapog_bam.changes" />
+            <output name="changes" file="hapog_bam.changes"/>
         </test>
     </tests>
     <help><![CDATA[
diff -r ee0d6e789958 -r 5287036a797a test-data/hapog_bam.changes
--- a/test-data/hapog_bam.changes	Sun Jan 28 23:46:07 2024 +0000
+++ b/test-data/hapog_bam.changes	Fri Apr 05 09:39:36 2024 +0000
@@ -1,3 +1,2 @@
 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=0.9752	ratio2=0.9752
 
diff -r ee0d6e789958 -r 5287036a797a test-data/hapog_bam.fasta
--- a/test-data/hapog_bam.fasta	Sun Jan 28 23:46:07 2024 +0000
+++ b/test-data/hapog_bam.fasta	Fri Apr 05 09:39:36 2024 +0000
@@ -274,6 +274,6 @@
 CATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC
 TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCT
 ACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACAT
-CTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGAC
+CTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGAC
 ATCACGATG