# HG changeset patch
# User richard-burhans
# Date 1713460632 0
# Node ID 9e34b25a8670300aeb3816b65dd00293810a8e43
# Parent  d3f11ae6790c3cec3018fc69db9ce9f20b95883d
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit 288c3e1887d4c13dcc922c612957460471977ff0

diff -r d3f11ae6790c -r 9e34b25a8670 diagonal_partition.py
--- a/diagonal_partition.py	Thu Apr 18 16:51:46 2024 +0000
+++ b/diagonal_partition.py	Thu Apr 18 17:17:12 2024 +0000
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python
 
 """
 Diagonal partitioning for segment files output by SegAlign.
diff -r d3f11ae6790c -r 9e34b25a8670 macros.xml
--- a/macros.xml	Thu Apr 18 16:51:46 2024 +0000
+++ b/macros.xml	Thu Apr 18 17:17:12 2024 +0000
@@ -7,7 +7,7 @@
         </requirements>
     </xml>
     <token name="@TOOL_VERSION@">0.1.2.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="edam_ontology">
         <edam_operations>
diff -r d3f11ae6790c -r 9e34b25a8670 run_segalign_diagonal_partition
--- a/run_segalign_diagonal_partition	Thu Apr 18 16:51:46 2024 +0000
+++ b/run_segalign_diagonal_partition	Thu Apr 18 17:17:12 2024 +0000
@@ -3,7 +3,6 @@
 set -o errexit
 set -o nounset
 set -o pipefail
-#set -o xtrace
 
 ##
 ## parse arguments
diff -r d3f11ae6790c -r 9e34b25a8670 segalign.xml
--- a/segalign.xml	Thu Apr 18 16:51:46 2024 +0000
+++ b/segalign.xml	Thu Apr 18 17:17:12 2024 +0000
@@ -30,7 +30,9 @@
 #if str($mode.mode_selector) == "segalign"
     #if str($mode.diagonal_partition_options.diagonal_partition) == "true"
         #set $segalign_mode = "segalign_diagonal_partition"
-        '$__tool_directory__/run_segalign_diagonal_partition'
+        ## explicitly calling bash to bypass a pulsar bug
+        ## https://github.com/galaxyproject/pulsar/issues/341
+        bash '$__tool_directory__/run_segalign_diagonal_partition'
             --tool_directory '$__tool_directory__'
             --max_segments '$mode.diagonal_partition_options.max_segments'
     #else