changeset 16:79182c2a8c80 draft default tip

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz commit e03d88240ee3894a2bb7bf2f196d9215cb8e0621

--- a/batched_lastz.xml	Mon Sep 08 22:32:10 2025 +0000
+++ b/batched_lastz.xml	Tue Sep 09 17:51:23 2025 +0000
@@ -12,9 +12,15 @@
             '--input=$input'
             '--output=$output'
             --parallel=\${GALAXY_SLOTS:-2}
+        #if $developer.debug_enabled
+            --debug
+        #end if
     ]]></command>
     <inputs>
         <param argument="--input" type="data" format="tgz" label="Tarball"/>
+        <section name="developer" title="Developer options" expanded="false">
+            <param name="debug_enabled" type="boolean" checked="false" label="Print debug messages"/>
+        </section>
     </inputs>
     <outputs>
         <data name="output" label="Batched LASTZ on ${on_string}" format="auto" />

--- a/macros.xml	Mon Sep 08 22:32:10 2025 +0000
+++ b/macros.xml	Tue Sep 09 17:51:23 2025 +0000
@@ -6,7 +6,7 @@
         </requirements>
     </xml>
     <token name="@TOOL_VERSION@">1.04.22</token>
-    <token name="@VERSION_SUFFIX@">5</token>
+    <token name="@VERSION_SUFFIX@">6</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="citations">
         <citations>

--- a/run_lastz_tarball.py	Mon Sep 08 22:32:10 2025 +0000
+++ b/run_lastz_tarball.py	Tue Sep 09 17:51:23 2025 +0000
@@ -226,10 +226,23 @@
         except FileNotFoundError:
             sys.exit(f"ERROR: input tarball missing galaxy/format.txt: {self.pathname}")
 
-        if format_name in ["axt", "bam", "maf"]:
-            self.format_name = format_name
-        elif format_name == "differences":
-            self.format_name = "interval"
+        format_map = {
+            "axt": "axt",
+            "axt+": "axt",
+            "cigar": "cigar",
+            "differences": "interval",
+            "lav": "lav",
+            "lav+text": "lav",
+            "maf": "maf",
+            "maf+": "maf",
+            "maf-": "maf",
+            "sam": "sam",
+            "sam-": "sam",
+            "softsam": "sam",
+            "softsam-": "sam"
+        }
+
+        self.format_name = format_map.get(format_name, "tabular")
 
 
 class TarRunner:
@@ -336,6 +349,8 @@
             while not output_queue.empty():
                 run_time = output_queue.get()
                 run_times.append(run_time)
+                if self.debug:
+                    print(f"lastz took {run_time}", file=sys.stderr, flush=True)
 
             if found_falures:
                 sys.exit("lastz command failed")