# HG changeset patch
# User galaxy-australia
# Date 1688527498 0
# Node ID 9eeb13a92d79d2bd44d57d3b4e26a543f0250f78
# Parent  2263989660f590a1cb6013f26cf599a2a0a83026
planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2d431863824af49c82ff2ae318abee3b16141a4e

diff -r 2263989660f5 -r 9eeb13a92d79 cactus_cactus.xml
--- a/cactus_cactus.xml	Mon May 15 04:34:02 2023 +0000
+++ b/cactus_cactus.xml	Wed Jul 05 03:24:58 2023 +0000
@@ -24,20 +24,22 @@
 
         #if $aln_mode.aln_mode_select == 'intraspecies':
             ## Run cactus-pangenome
+            ## --reference should be the first argument
+            ## https://github.com/ComparativeGenomicsToolkit/cactus/issues/1093#issuecomment-1620088688
             cactus-pangenome 
+            --reference $aln_mode.ref_level
             --binariesMode local
-            --maxCores  \${GALAXY_SLOTS:-4}
+            --maxCores \${GALAXY_SLOTS:-4}
             --maxMemory \${GALAXY_MEMORY_MB:-8192}M    
             --outDir ./
             --outName alignment
-            --reference $aln_mode.ref_level
-            ./jobStore
+            jobStore
             seqfile.txt
         #else if $aln_mode.aln_mode_select == 'interspecies':
             ## Run cactus normally
             cactus 
             --binariesMode local 
-            --maxCores  \${GALAXY_SLOTS:-4}
+            --maxCores \${GALAXY_SLOTS:-4}
             --maxMemory \${GALAXY_MEMORY_MB:-8192}M
             --workDir ./
             jobStore
@@ -177,12 +179,12 @@
             </repeat>
             <output name="out_hal">
                 <assert_contents>
-                    <has_size value="7420424" delta="200000" />
+                    <has_size value="6235006" delta="200000" />
                 </assert_contents>
             </output>
             <output name="out_gfa">
                 <assert_contents>
-                    <has_size value="5786846" delta="200000" />
+                    <has_size value="5771414" delta="200000" />
                 </assert_contents>
             </output>
         </test>
diff -r 2263989660f5 -r 9eeb13a92d79 macros.xml
--- a/macros.xml	Mon May 15 04:34:02 2023 +0000
+++ b/macros.xml	Wed Jul 05 03:24:58 2023 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.5.1</token>
+    <token name="@TOOL_VERSION@">2.6.4</token>
     <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">20.09</token>
     <xml name="requirements">