--- a/cactus_export.xml	Mon Aug 28 23:09:49 2023 +0000
+++ b/cactus_export.xml	Thu Feb 08 08:52:41 2024 +0000
@@ -6,13 +6,12 @@
     <expand macro="xrefs"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-        export TMPDIR=\${_GALAXY_JOB_TMP_DIR} &&
 
         ## check if the reference level was specified
         #if $export_select.format in ['maf_selector', 'vg_selector']:
             #if $export_select.ref_level == '':
                 echo "You must provide a reference level" &&
-                exit 1
+                exit 1 ;
             #end if
         #end if
 
@@ -32,7 +31,7 @@
             &&
             hal2assemblyHub.py 
             --maxCores  \${GALAXY_SLOTS:-4}
-            --maxMemory \${GALAXY_MEMORY_MB:-8192}M
+            --maxMemory \${GALAXY_MEMORY_MB:-8196}M
             ./jobStore
             alignment.hal
             assemblyhub
@@ -50,7 +49,7 @@
 
     ]]></command>
     <inputs>
-        <param name="hal_file" type="data" format="h5" label="HAL file" help="Multiple-genome alignment generated by Cactus" />
+        <param name="hal_file" type="data" format="h5" label="HAL file" help="Multiple-genome alignment generated by Cactus"/>
         <conditional name="export_select">
             <param name="format" type="select" label="Output format" help="The type of output you want to export. Run this tool once for each output format.">
                 <option value="maf_selector" selected="true">MAF file</option>
@@ -58,23 +57,23 @@
                 <option value="vg_selector">VG file</option>
             </param>
             <when value="maf_selector">
-                <param name="ref_level" type="text" value="" label="Reference genome" help="Specify one of the Input Genomes as the reference level. This must match the label used in 'Genome Label'." />
+                <param name="ref_level" type="text" value="" label="Reference genome" help="Specify one of the Input Genomes as the reference level. This must match the label used in 'Genome Label'."/>
             </when>
             <when value="ah_selector">
             </when>
             <when value="vg_selector">
-                <param name="ref_level" type="text" value="" label="Reference genome" help="Specify one of the Input Genomes as the reference level. This must match the label used in 'Genome Label'." />
+                <param name="ref_level" type="text" value="" label="Reference genome" help="Specify one of the Input Genomes as the reference level. This must match the label used in 'Genome Label'."/>
             </when>
         </conditional>
     </inputs>
     <outputs>
-        <data name="out_maf" format="maf" from_work_dir="alignment.maf" label="${tool.name} on ${on_string} (MAF file)" >
+        <data name="out_maf" format="maf" from_work_dir="alignment.maf" label="${tool.name} on ${on_string} (MAF file)">
             <filter>export_select['format'] == 'maf_selector'</filter>
         </data>
-        <data name="out_vg" format="vg" from_work_dir="alignment.pg" label="${tool.name} on ${on_string} (VG file)" >
+        <data name="out_vg" format="vg" from_work_dir="alignment.pg" label="${tool.name} on ${on_string} (VG file)">
             <filter>export_select['format'] == 'vg_selector'</filter>
         </data>
-        <data name="out_ah" format="tar" from_work_dir="assemblyhub.tar" label="${tool.name} on ${on_string} (Assembly Hub)" >
+        <data name="out_ah" format="tar" from_work_dir="assemblyhub.tar" label="${tool.name} on ${on_string} (Assembly Hub)">
             <filter>export_select['format'] == 'ah_selector'</filter>
         </data>
     </outputs>
@@ -82,34 +81,34 @@
         <!-- this fails because no reference level is set -->
         <test expect_failure="true">
             <conditional name="export_select">
-                <param name="format" value="maf_selector" />
+                <param name="format" value="maf_selector"/>
             </conditional>
-            <param name="hal_file" ftype="h5" value="evolverMammals.hal" />
+            <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/evolverMammals.hal"/>
         </test>
         <!-- within-species mode -->
         <test expect_num_outputs="1">
             <conditional name="export_select">
-                <param name="ref_level" value="simMouse_chr6" />
-                <param name="format" value="maf_selector" />
+                <param name="ref_level" value="simMouse_chr6"/>
+                <param name="format" value="maf_selector"/>
             </conditional>
-            <param name="hal_file" ftype="h5" value="within.hal" />
-            <output name="out_maf" file="set_reference.maf" />
+            <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/within.hal"/>
+            <output name="out_maf" location="https://zenodo.org/record/8336793/files/set_reference.maf"/>
         </test>
         <!-- between-species  -->
         <test expect_num_outputs="1">
             <conditional name="export_select">
-                <param name="ref_level" value="simMouse_chr6" />
-                <param name="format" value="maf_selector" />
+                <param name="ref_level" value="simMouse_chr6"/>
+                <param name="format" value="maf_selector"/>
             </conditional>
-            <param name="hal_file" ftype="h5" value="evolverMammals_noroot.hal" />
-            <output name="out_maf" file="evolverMammals_noroot.maf" />
+            <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/evolverMammals_noroot.hal"/>
+            <output name="out_maf" location="https://zenodo.org/record/8336793/files/evolverMammals_noroot.maf"/>
         </test>
         <!-- assembly hub format -->
         <test expect_num_outputs="1">
             <conditional name="export_select">
-                <param name="format" value="ah_selector" />
+                <param name="format" value="ah_selector"/>
             </conditional>
-            <param name="hal_file" ftype="h5" value="within.hal" />
+            <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/within.hal"/>
             <output name="out_ah">
                 <assert_contents>
                     <has_archive_member path="assemblyhub/hub.txt"/>
@@ -119,13 +118,13 @@
         <!-- vg format -->
         <test expect_num_outputs="1">
             <conditional name="export_select">
-                <param name="format" value="vg_selector" />
-                <param name="ref_level" value="simMouse_chr6" />
+                <param name="format" value="vg_selector"/>
+                <param name="ref_level" value="simMouse_chr6"/>
             </conditional>
-            <param name="hal_file" ftype="h5" value="within.hal" />            
+            <param name="hal_file" ftype="h5" location="https://zenodo.org/record/8336793/files/within.hal"/>
             <output name="out_vg">
                 <assert_contents>
-                        <has_size value="860452" delta="200000" />
+                    <has_size value="860452" delta="200000"/>
                 </assert_contents>
             </output>
         </test>