From 84dced1e7b63408b7309d170453a0b37f54d6beb Mon Sep 17 00:00:00 2001
From: Wolfgang Maier <maierw@informatik.uni-freiburg.de>
Date: Sat, 9 Nov 2024 10:51:23 +0100
Subject: [PATCH 1/2] Fix wrapper name

---
 tools/irma/{irma.ml => irma.xml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename tools/irma/{irma.ml => irma.xml} (100%)

diff --git a/tools/irma/irma.ml b/tools/irma/irma.xml
similarity index 100%
rename from tools/irma/irma.ml
rename to tools/irma/irma.xml

From 3a1dd549c6abc105b34aa3e1f6504a2710647037 Mon Sep 17 00:00:00 2001
From: Wolfgang Maier <maierw@informatik.uni-freiburg.de>
Date: Sat, 9 Nov 2024 11:23:19 +0100
Subject: [PATCH 2/2] Fix slots handling and optional outputs

---
 tools/irma/irma.xml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/tools/irma/irma.xml b/tools/irma/irma.xml
index d7c00326f40..b26b7ec49dd 100644
--- a/tools/irma/irma.xml
+++ b/tools/irma/irma.xml
@@ -44,12 +44,13 @@ IRMA '${module}'
 resultDir &&
 ## IRMA does not write empty output files
 ## so the following script makes sure all expected outputs exist unconditionally
-python3 '$__tool_directory__/createMissingFiles.py'
+python3 '$__tool_directory__/createMissingFiles.py' &&
+cat irma_config.sh
     ]]></command>
     <configfiles>
         <configfile filename='irma_config.sh'><![CDATA[
 SINGLE_LOCAL_PROC=\${GALAXY_SLOTS:-1}
-DOUBLE_LOCAL_PROC=$((GALAXY_SLOTS/2 + (GALAXY_SLOTS==1)))
+DOUBLE_LOCAL_PROC=\$((SINGLE_LOCAL_PROC/2 + (SINGLE_LOCAL_PROC==1)))
 TMP=\$TMPDIR
 #if $advanced_config.customize == 'yes':
   #if $advanced_config.reference == 'yes':
@@ -277,7 +278,7 @@ SIG_LEVEL=$advanced_config.variant_calling.SIG_LEVEL
         </collection>
         <!-- optional outputs-->
         <collection name="bam_collection" type="list" label="Alignment files (bam)">
-            <filter>'bam' in optional_outputs</filter>
+            <filter>optional_outputs and 'bam' in optional_outputs</filter>
             <data name="PB1" format="bam" from_work_dir="resultDir/A_PB1.bam" label="PB1"/>
             <data name="PB2" format="bam" from_work_dir="resultDir/A_PB2.bam" label="PB2"/>
             <data name="PA" format="bam" from_work_dir="resultDir/A_PA.bam" label="PA"/>
@@ -288,7 +289,7 @@ SIG_LEVEL=$advanced_config.variant_calling.SIG_LEVEL
             <data name="NS" format="bam" from_work_dir="resultDir/A_NS.bam" label="NS"/>
         </collection>
         <collection name="vcf_collection" type="list" label="Variant calling files (VCF)">
-            <filter>'vcf' in optional_outputs</filter>
+            <filter>optional_outputs and 'vcf' in optional_outputs</filter>
             <data name="PB1" format="vcf" from_work_dir="resultDir/A_PB1.vcf" label="PB1"/>
             <data name="PB2" format="vcf" from_work_dir="resultDir/A_PB2.vcf" label="PB2"/>
             <data name="PA" format="vcf" from_work_dir="resultDir/A_PA.vcf" label="PA"/>