final fixes

richard-burhans · May 1, 2024 · 3bbc9b9 · 3bbc9b9
1 parent fc8b75c
commit 3bbc9b9
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Showing 2 changed files with 9 additions and 2 deletions.
diff --git a/tools/batched_lastz/batched_lastz.xml b/tools/batched_lastz/batched_lastz.xml
@@ -1,11 +1,18 @@
+
 <tool id="batched_lastz" name="Batched Lastz" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>: align batches of sequences</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
+    <required_files>
+        <include path="run_lastz_tarball.py"/>
+    </required_files>
     <command detect_errors="exit_code"><![CDATA[
-        run_lastz_tarball.py '--input=$input' '--output=$output' '--parallel=\${GALAXY_SLOTS:-2}'
+        python '$__tool_directory__/run_lastz_tarball.py'
+            '--input=$input'
+            '--output=$output'
+            --parallel=\${GALAXY_SLOTS:-2}
     ]]></command>
     <inputs>
         <param argument="--input" type="data" format="tgz" label="Tarball"/>

diff --git a/tools/batched_lastz/run_lastz_tarball.py b/tools/batched_lastz/run_lastz_tarball.py
@@ -323,7 +323,7 @@ def main() -> None:
     parser = argparse.ArgumentParser()
     parser.add_argument("--input", type=str, required=True)
     parser.add_argument("--output", type=str, required=True)
-    parser.add_argument("--parallel", type=int, default=1, required=False)
+    parser.add_argument("--parallel", type=int, default=2, required=False)
     parser.add_argument("--debug", action="store_true", required=False)
 
     args = parser.parse_args()