Mercurial > repos > bgruening > bionano_scaffold

comparison 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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10:22286dab5aa1 11:3371c5bdc17a
58 #if $trim_cut_sites 58 #if $trim_cut_sites
59 && export PATH=/opt/conda/bin/:\$PATH 59 && export PATH=/opt/conda/bin/:\$PATH
60 && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_NCBI 'SCAFFOLD_NCBI_trimmed.fasta' 'output.log' 60 && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_NCBI 'SCAFFOLD_NCBI_trimmed.fasta' 'output.log'
61 && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_not_scaffolded 'NOT_SCAFFOLDED_trimmed.fasta' 'output.log' 61 && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_not_scaffolded 'NOT_SCAFFOLDED_trimmed.fasta' 'output.log'
62 #end if 62 #end if
63 && echo >> hybrid_scaffolds/*cut.txt 63 ## the next lines are required because the XXXX_cut.txt file is not always generated
64 && mv hybrid_scaffolds/*cut.txt hybrid_scaffolds/keys.txt 64 && touch hybrid_scaffolds/temp_cut.txt
65 && cat hybrid_scaffolds/*cut.txt > hybrid_scaffolds/keys.txt
65 ]]> </command> 66 ]]> </command>
66 <configfiles> 67 <configfiles>
67 <configfile name="vgp_mode"><![CDATA[ 68 <configfile name="vgp_mode"><![CDATA[
68 #if $configuration_options.configuration == 'vgp' 69 #if $configuration_options.configuration == 'vgp'
69 <hybridScaffold> 70 <hybridScaffold>