From efaed3f0dfb59b55f85d51c5f4d91b8187083aeb Mon Sep 17 00:00:00 2001
From: Tom Harrop <tharrop@unimelb.edu.au>
Date: Mon, 18 Sep 2023 16:02:35 +1000
Subject: [PATCH 1/3] reduce amount of allocated ram passed to abyss

---
 tools/abyss/abyss-pe.xml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tools/abyss/abyss-pe.xml b/tools/abyss/abyss-pe.xml
index f09040360f4..142a06c6ca6 100644
--- a/tools/abyss/abyss-pe.xml
+++ b/tools/abyss/abyss-pe.xml
@@ -2,7 +2,7 @@
     <description>de novo sequence assembler</description>
     <macros>
         <token name="@TOOL_VERSION@">2.3.6</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <xml name="reads_conditional">
             <conditional name="reads">
                 <param name="reads_selector" type="select" label="Type of paired-end datasets">
@@ -85,7 +85,8 @@
 abyss-pe
 name=abyss
 j=\${GALAXY_SLOTS:-1}
-B=\${GALAXY_MEMORY_MB:-2048}M
+B=\$((\${GALAXY_MEMORY_MB:-2048} * 8 /10 ))M
+
 k=$k
 
 #if str($K)

From 9ad6b6c5b775f2dca032fe04f3535d0268941615 Mon Sep 17 00:00:00 2001
From: Tom Harrop <tharrop@unimelb.edu.au>
Date: Mon, 18 Sep 2023 16:06:29 +1000
Subject: [PATCH 2/3] make that 90

---
 tools/abyss/abyss-pe.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/abyss/abyss-pe.xml b/tools/abyss/abyss-pe.xml
index 142a06c6ca6..d7c9d0d5907 100644
--- a/tools/abyss/abyss-pe.xml
+++ b/tools/abyss/abyss-pe.xml
@@ -85,7 +85,7 @@
 abyss-pe
 name=abyss
 j=\${GALAXY_SLOTS:-1}
-B=\$((\${GALAXY_MEMORY_MB:-2048} * 8 /10 ))M
+B=\$((\${GALAXY_MEMORY_MB:-2048} * 9 /10 ))M
 
 k=$k
 

From 92d5ff33abf80d934d122a1e1414a37381043b2b Mon Sep 17 00:00:00 2001
From: Tom Harrop <tharrop@unimelb.edu.au>
Date: Mon, 18 Sep 2023 17:25:34 +1000
Subject: [PATCH 3/3] linting

---
 tools/abyss/abyss-pe.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/abyss/abyss-pe.xml b/tools/abyss/abyss-pe.xml
index d7c9d0d5907..9c12289d38e 100644
--- a/tools/abyss/abyss-pe.xml
+++ b/tools/abyss/abyss-pe.xml
@@ -228,7 +228,7 @@ k=$k
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="5">
             <repeat name="lib_repeat">
                 <conditional name="reads">
                     <param name="reads_selector" value="paired" />
@@ -243,14 +243,14 @@ k=$k
             <output name="indels" file="empty_file.fasta" />
             <output name="stats" file="abyss-stats1.tab" />
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="se_reads" ftype="fastq.gz" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" />
             <param name="k" value="50" />
             <output name="unitigs" file="abyss-unitigs2.fa" />
             <output name="indels" file="empty_file.fasta" />
             <output name="stats" file="abyss-stats2.tab" />
         </test>
-        <test>
+        <test expect_num_outputs="4">
             <param name="se_reads" ftype="fasta" value="assembly_sample-R1.fasta,assembly_sample-R2.fasta" />
             <param name="long_seqs" ftype="fasta" value="assembly_sample-R2.fasta" />
             <param name="k" value="50" />