Mercurial > repos > greg > assembly_post_processor

changeset 95:7801f23bc5d9 draft

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Uploaded
author greg
date Thu, 26 Oct 2017 11:41:10 -0400
parents 33915a72ae4e
children 11e85af74c7e
files assembly_post_processor.xml
diffstat 1 files changed, 7 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/assembly_post_processor.xml	Thu Oct 26 11:39:10 2017 -0400
+++ b/assembly_post_processor.xml	Thu Oct 26 11:41:10 2017 -0400
@@ -34,17 +34,17 @@
     --min_length $options_type.min_length
 #end if
 --num_threads \${GALAXY_SLOTS:-4}
-&& mv $output_dir/transcripts.cds '$output_cds'
-&& mv $output_dir/transcripts.pep '$output_pep'
-&& mv $output_dir/transcripts.cleaned.cds '$output_cleaned_cds'
-&& mv $output_dir/transcripts.cleaned.pep '$output_cleaned_pep'
+&& cp $output_dir/transcripts.cds '$output_cds'
+&& cp $output_dir/transcripts.pep '$output_pep'
+&& cp $output_dir/transcripts.cleaned.cds '$output_cleaned_cds'
+&& cp $output_dir/transcripts.cleaned.pep '$output_cleaned_pep'
 #if str($options_type.options_type_selector) == 'advanced':
     #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
-        && mv $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'
+        && cp $output_dir/targeted_gene_family_assemblies.stats '$output_targeted_gene_families_stats'
     #end if
     #if str($options_type.dereplicate) == 'yes':
-        && mv $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'
-        && mv $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'
+        && cp $output_dir/transcripts.cleaned.nr.cds '$output_cleaned_nr_cds'
+        && cp $output_dir/transcripts.cleaned.nr.pep '$output_cleaned_nr_pep'
     #end if
 #end if
     ]]></command>