# HG changeset patch
# User richard-burhans
# Date 1720889512 0
# Node ID ae2cd39594ebe919d165476d1a7cadbf048b63db
# Parent  e6fde4082c76833a06f2563b4430d79175e6015f
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit 195ced408efbb08aaeccf05135c27364372b299f

diff -r e6fde4082c76 -r ae2cd39594eb runner.py
--- a/runner.py	Sat Jul 13 15:43:14 2024 +0000
+++ b/runner.py	Sat Jul 13 16:51:52 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))?(?: --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")
+    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")
 
     def __init__(self, line: str) -> None:
         self.line = line