# HG changeset patch
# User greg
# Date 1484061378 18000
# Node ID 038777896b71fac61e70bea1ea24e62ee483c7bc
# Parent  c4a9c23334a499d66a726a04b76c8b6f32b2b133
Uploaded

diff -r c4a9c23334a4 -r 038777896b71 gene_family_classifier.xml
--- a/gene_family_classifier.xml	Tue Jan 10 09:53:25 2017 -0500
+++ b/gene_family_classifier.xml	Tue Jan 10 10:16:18 2017 -0500
@@ -24,16 +24,18 @@
                     #set create_corresponding_coding_sequences = True
                 #else:
                     #set create_corresponding_coding_sequences = False
-                #endif
+                #end if
                 mkdir -p $dest_dir &&
             #else:
                 #set create_ortho_sequences = False
             #end if
+
             GeneFamilyClassifier
             --proteins "$input"
             --scaffold "$scaffold"
             --method $method
             --classifier $save_hmmscan_log_cond.classifier
+
             #if str($options_type.options_type_selector) == 'advanced':
                 --super_orthogroups $options_type.super_orthogroups
                 #if str($options_type.single_copy_cond) == 'taxa':
@@ -47,8 +49,10 @@
                     #end if
                 #end if
             #end if
+
             --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
             --num_threads "\${GALAXY_SLOTS:-4}"
+
             #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both':
                 #if str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes':
                     && mv geneFamilyClassification_dir/hmmscan.log $hmmscan_log
@@ -56,6 +60,7 @@
                     && rm geneFamilyClassification_dir/hmmscan.log
                 #end if
             #end if
+
             #if $create_ortho_sequences:
                 #if $create_corresponding_coding_sequences:
                     && echo "Sequences classified into pre-computed orthologous plant gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | wc -l` files" > $output
@@ -65,6 +70,7 @@
                 && ls $orthogroups_fasta_src_dir >> $output
                 && mv $orthogroups_fasta_src_dir/* $dest_dir
             #end if
+
         ]]>
     </command>
     <inputs>