Merge pull request #91 from TomHarrop/cactus_2.6.4

cactus_2.6.4
usegalaxy-au · Jul 5, 2023 · 2d43186 · 2d43186
2 parents c1aaee9 + 375a03e
commit 2d43186
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Showing 3 changed files with 10 additions and 8 deletions.
diff --git a/tools/cactus/cactus_cactus.xml b/tools/cactus/cactus_cactus.xml
@@ -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 --git a/tools/cactus/cactus_export.xml b/tools/cactus/cactus_export.xml
@@ -80,7 +80,7 @@
     </outputs>
     <tests>
         <!-- this fails because no reference level is set -->
-        <test expect_num_outputs="1" expect_failure="true">
+        <test expect_failure="true">
             <conditional name="export_select">
                 <param name="format" value="maf_selector" />
             </conditional>

diff --git a/tools/cactus/macros.xml b/tools/cactus/macros.xml
@@ -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">