Mercurial > repos > greg > gene_family_classifier

changeset 8:d678d4c2e9e1 draft

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Uploaded
author greg
date Wed, 21 Dec 2016 10:13:04 -0500
parents 4415ee993192
children c7010d37df2c
files gene_family_classifier.xml
diffstat 1 files changed, 7 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/gene_family_classifier.xml	Tue Dec 20 14:37:06 2016 -0500
+++ b/gene_family_classifier.xml	Wed Dec 21 10:13:04 2016 -0500
@@ -12,9 +12,11 @@
     </stdio>
     <command>
         <![CDATA[
-            #if str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
-                #set orthogroups_fasta_dir = $options_type.create_orthogroup_cond.coding_sequences.extra_files_path
-                mkdir -p $orthogroups_fasta_dir &&
+            #if str($options_type.options_type_selector) == 'advanced' and str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
+                #import os
+                #set orthogroups_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
+                #set orthogroups_dest_dir = $options_type.create_orthogroup_cond.coding_sequences.extra_files_path
+                mkdir -p $orthogroups_dest_dir &&
             #end if
             GeneFamilyClassifier
             --proteins "$input"
@@ -34,8 +36,8 @@
             #end if
             --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
             --num_threads \${GALAXY_SLOTS:-4}
-            #if str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
-                && cp "./geneFamilyClassification_dir/orthogroups_fasta/*" $orthogroups_fasta_dir
+            #if str($options_type.options_type_selector) == 'advanced' and str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
+                && mv $orthogroups_src_dir/* $orthogroups_dest_dir
             #end if
         ]]>
     </command>