# HG changeset patch
# User richard-burhans
# Date 1722393651 0
# Node ID a5769923297cee1e09184376b00022e2ea62747b
# Parent  52a13f003b2dbef9e502b0845d9e0f44d4a522c8
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit 6930a27f7d40399b1fd14ed7b8c6c6128e2d97ca

diff -r 52a13f003b2d -r a5769923297c runner.py
--- a/runner.py	Tue Jul 30 17:25:08 2024 +0000
+++ b/runner.py	Wed Jul 31 02:40:51 2024 +0000
@@ -37,7 +37,7 @@
 
 
 class LastzCommand:
-    lastz_command_regex = re.compile(r"lastz (.+?)?ref\.2bit\[nameparse=darkspace\]\[multiple\]\[subset=ref_block(\d+)\.name\] (.+?)?query\.2bit\[nameparse=darkspace\]\[subset=query_block(\d+)\.name] --format=(\S+) --ydrop=(\d+) --gappedthresh=(\d+) --strand=(minus|plus)(?: --ambiguous=(\S+))?(?: --(notrivial))?(?: --scores=(\S+))? --segments=tmp(\d+)\.block(\d+)\.r(\d+)\.(minus|plus)(?:\.split(\d+))?\.segments --output=tmp(\d+)\.block(\d+)\.r(\d+)\.(minus|plus)(?:\.split(\d+))?\.(\S+) 2> tmp(\d+)\.block(\d+)\.r(\d+)\.(minus|plus)(?:\.split(\d+))?\.err")
+    lastz_command_regex = re.compile(r"lastz (.+?)?ref\.2bit\[nameparse=darkspace\]\[multiple\]\[subset=ref_block(\d+)\.name\] (.+?)?query\.2bit\[nameparse=darkspace\]\[subset=query_block(\d+)\.name] --format=(\S+) --ydrop=(\d+) --gappedthresh=(\d+) --strand=(minus|plus)(?: --ambiguous=(\S+))?(?: --(notrivial))?(?: --scoring=(\S+))? --segments=tmp(\d+)\.block(\d+)\.r(\d+)\.(minus|plus)(?:\.split(\d+))?\.segments --output=tmp(\d+)\.block(\d+)\.r(\d+)\.(minus|plus)(?:\.split(\d+))?\.(\S+) 2> tmp(\d+)\.block(\d+)\.r(\d+)\.(minus|plus)(?:\.split(\d+))?\.err")
 
     def __init__(self, line: str) -> None:
         self.line = line