# HG changeset patch
# User greg
# Date 1483540842 18000
# Node ID fd6773b7bb3fff1181c246b99294813282b0fce0
# Parent  56ff8d7064144874a7f7f885191f21700b796ab9
Uploaded

diff -r 56ff8d706414 -r fd6773b7bb3f phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Wed Jan 04 09:31:35 2017 -0500
+++ b/phylogenomics_analysis.xml	Wed Jan 04 09:40:42 2017 -0500
@@ -12,6 +12,10 @@
     </stdio>
     <command>
         <![CDATA[
+            #import os
+            #set src_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta')
+            #set dest_dir = $output.extra_files_path
+            mkdir -p $dest_dir &&
             PhylogenomicsAnalysis
             --orthogroup_faa "$orthogroup_fna.extra_files_path"
             --scaffold "$scaffold"
@@ -61,9 +65,9 @@
             #end if
             --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
             --num_threads \${GALAXY_SLOTS:-4} &&
-            echo "Sequence alignments and corresponding phylogenies: `ls -l phylogenomicsAnalysis_dir/orthogroups_fasta | wc -l` files" > $output &&
-            ls phylogenomicsAnalysis_dir/orthogroups_fasta >> $output &&
-            mv phylogenomicsAnalysis_dir/orthogroups_fasta/* $output.extra_files_path
+            echo "Sequence alignments and corresponding phylogenies: `ls $src_dir | wc -l` files" > $output &&
+            ls $src_dir >> $output &&
+            mv $src_dir/* $dest_dir
         ]]>
     </command>
     <inputs>