Mercurial > repos > bgruening > bionano_scaffold

diff bionano_scaffold.xml @ 11:3371c5bdc17a draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit f2952aec50c8bf269f95bd3caa634b232e640729
author bgruening
date Mon, 27 Feb 2023 14:32:45 +0000
parents 22286dab5aa1
children
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--- 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[