# HG changeset patch
# User greg
# Date 1487769592 18000
# Node ID 5de38d2ef87e513de5a87da32056d1547fe6f427
# Parent  bfc2eb2906f2220335035370a38cb93a35bfe8cc
Uploaded

diff -r bfc2eb2906f2 -r 5de38d2ef87e gene_family_classifier.xml
--- a/gene_family_classifier.xml	Wed Feb 22 08:16:45 2017 -0500
+++ b/gene_family_classifier.xml	Wed Feb 22 08:19:52 2017 -0500
@@ -112,11 +112,11 @@
 
             #if $create_ortho_sequences:
                 #if $create_corresponding_coding_sequences:
-                    && echo -e "#Size\tName" > $output_ptorthocs
-                    && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t<a href=\"$orthogroups_fasta_dest_dir/"$9"\">"$9"</a><br/>"}' >> $output_ptorthocs
+                    && echo -e "#Size\tName<br/>" > $output_ptorthocs
+                    && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t<a href=\"$output_ptorthocs.extra_files_path/"$9"\">"$9"</a><br/>"}' >> $output_ptorthocs
                 #else:
                     && echo -e "#Size\tName" > $output_ptortho
-                    && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t<a href=\"$orthogroups_fasta_dest_dir/"$9"\">"$9"</a><br/>"}' >> $output_ptortho
+                    && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t<a href=\"$output_ptortho.extra_files_path/"$9"\">"$9"</a><br/>"}' >> $output_ptortho
                 #end if
                 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir || true
             #end if
@@ -124,7 +124,7 @@
             #if $single_copy_orthogroup:
                 #if $create_ortho_sequences:
                     && echo -e "#Size\tName" > $output_ptsco
-                    && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t<a href=\"$single_copy_fasta_dest_dir/"$9"\">"$9"</a><br/>"}' >> $output_ptsco
+                    && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t<a href=\"$output_ptsco.extra_files_path/"$9"\">"$9"</a><br/>"}' >> $output_ptsco
                     && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir || true
                 #end if
             #end if