# HG changeset patch
# User bgruening
# Date 1677508365 0
# Node ID 3371c5bdc17a751b362b10aae2b558040b213ea0
# Parent  22286dab5aa1f9ee88beeace458c75ca36af7e12
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f2952aec50c8bf269f95bd3caa634b232e640729

diff -r 22286dab5aa1 -r 3371c5bdc17a bionano_scaffold.xml
--- a/bionano_scaffold.xml	Wed Jan 18 15:22:13 2023 +0000
+++ b/bionano_scaffold.xml	Mon Feb 27 14:32:45 2023 +0000
@@ -60,8 +60,9 @@
             && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_NCBI 'SCAFFOLD_NCBI_trimmed.fasta' 'output.log'
             && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_not_scaffolded 'NOT_SCAFFOLDED_trimmed.fasta' 'output.log'
         #end if
-        && echo >> hybrid_scaffolds/*cut.txt
-        && mv hybrid_scaffolds/*cut.txt hybrid_scaffolds/keys.txt
+        ## the next lines are required because the XXXX_cut.txt file is not always generated
+        && touch hybrid_scaffolds/temp_cut.txt
+        && cat hybrid_scaffolds/*cut.txt > hybrid_scaffolds/keys.txt
     ]]>    </command>
     <configfiles>
         <configfile name="vgp_mode"><![CDATA[
diff -r 22286dab5aa1 -r 3371c5bdc17a macros.xml
--- a/macros.xml	Wed Jan 18 15:22:13 2023 +0000
+++ b/macros.xml	Mon Feb 27 14:32:45 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">3.7.0</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@BIONANO_SUPPORT_TEXT@">
 Bionano Genomics has agreed to provide the licensed Bionano Solve
 software to enable the VGP to package the software in a container.