changeset 15:f6090d2a5722 draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz commit 439b32f4ac520e4b22770fa2becd363230e198e0

--- a/batched_lastz.xml	Fri Aug 30 15:32:44 2024 +0000
+++ b/batched_lastz.xml	Mon Sep 08 22:32:10 2025 +0000
@@ -22,7 +22,12 @@
     <tests>
       <test expect_num_outputs="1">
         <param name="input" value="input.tgz" ftype="tgz"/>
-        <output name="output" decompress="true" file="output.maf.gz" ftype="maf"/>
+        <output name="output">
+            <assert_contents>
+                <has_size min="1"/>
+            </assert_contents>
+        </output>
+
       </test>
     </tests>
     <help><![CDATA[

--- a/macros.xml	Fri Aug 30 15:32:44 2024 +0000
+++ b/macros.xml	Mon Sep 08 22:32:10 2025 +0000
@@ -6,7 +6,7 @@
         </requirements>
     </xml>
     <token name="@TOOL_VERSION@">1.04.22</token>
-    <token name="@VERSION_SUFFIX@">4</token>
+    <token name="@VERSION_SUFFIX@">5</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="citations">
         <citations>

--- a/run_lastz_tarball.py	Fri Aug 30 15:32:44 2024 +0000
+++ b/run_lastz_tarball.py	Mon Sep 08 22:32:10 2025 +0000
@@ -2,6 +2,8 @@
 
 import argparse
 import concurrent.futures
+import contextlib
+import gzip
 import json
 import multiprocessing
 import os
@@ -16,6 +18,16 @@
 import typing
 
 
[e-mail]
+def open_file(filename: str):
+    if filename.endswith(".gz"):
+        with gzip.open(filename, "wt", compresslevel=6) as f:
+            yield f
+    else:
+        with open(filename, "w") as f:
+            yield f
+
+
 lastz_output_format_regex = re.compile(
     r"^(?:axt\+?|blastn|cigar|differences|general-?.+|lav|lav\+text|maf[-+]?|none|paf(?::wfmash)?|rdotplot|sam-?|softsam-?|text)$",
     re.IGNORECASE,
@@ -214,7 +226,7 @@
         except FileNotFoundError:
             sys.exit(f"ERROR: input tarball missing galaxy/format.txt: {self.pathname}")
 
-        if format_name in ["bam", "maf"]:
+        if format_name in ["axt", "bam", "maf"]:
             self.format_name = format_name
         elif format_name == "differences":
             self.format_name = "interval"
@@ -341,10 +353,12 @@
             sys.exit(f"ERROR: expecting a single output file, found {num_output_files}")
 
         final_output_format = self.batch_tar.final_output_format()
+        if final_output_format in ["axt", "maf"]:
+            final_output_format = f"{final_output_format}.gz"
 
         for file_type, file_list in self.output_files.items():
-            with open(f"output.{final_output_format}", "w") as ofh:
-                if final_output_format == "maf":
+            with open_file(f"output.{final_output_format}") as ofh:
+                if final_output_format == "maf.gz":
                     print("##maf version=1", file=ofh)
 
                 for filename in file_list: