# HG changeset patch
# User greg
# Date 1486657763 18000
# Node ID dd22169524ee84a996b724133bf77db2e8f39c60
# Parent  ffaedadf9c185896c1060d975bbaef427725bf5f
Uploaded

diff -r ffaedadf9c18 -r dd22169524ee gene_family_classifier.xml
--- a/gene_family_classifier.xml	Thu Feb 09 10:53:31 2017 -0500
+++ b/gene_family_classifier.xml	Thu Feb 09 11:29:23 2017 -0500
@@ -41,10 +41,10 @@
 
                     #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes':
                         #set create_corresponding_coding_sequences = True
-                        #set orthogroups_fasta_dest_dir = $output_ptcgfcs.extra_files_path
+                        #set orthogroups_fasta_dest_dir = $output_ptorthocs.extra_files_path
                     #else:
                         #set create_corresponding_coding_sequences = False
-                        #set orthogroups_fasta_dest_dir = $output_ptcgf.extra_files_path
+                        #set orthogroups_fasta_dest_dir = $output_ptortho.extra_files_path
                     #end if
                     mkdir -p $orthogroups_fasta_dest_dir &&
                 #else:
@@ -107,9 +107,9 @@
 
             #if $create_ortho_sequences:
                 #if $create_corresponding_coding_sequences:
-                    && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgfcs
+                    && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptorthocs
                 #else:
-                    && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgf
+                    && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptortho
                 #end if
                 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir
             #end if
@@ -227,14 +227,18 @@
         <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}">
             <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter>
         </data>
-        <data name="output_ptcgf" format="ptcgf" label="Gene family clusters on ${on_string}">
+        <data name="output_ptortho" format="ptortho" label="Gene family clusters on ${on_string}">
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['create_orthogroup_cond']['create_corresponding_coding_sequences_cond']['create_corresponding_coding_sequences'] == 'no'</filter>
         </data>
-        <data name="output_ptcgfcs" format="ptcgfcs" label="Gene family clusters and corresponding coding sequences on ${on_string}">
+        <data name="output_ptorthocs" format="ptorthocs" label="Gene family clusters and corresponding coding sequences on ${on_string}">
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['create_orthogroup_cond']['create_corresponding_coding_sequences_cond']['create_corresponding_coding_sequences'] == 'yes'</filter>
         </data>
-        <data name="output_ptsco" format="txt" label="Single copy orthogroups on ${on_string}">
+        <data name="output_ptsco" format="tabular" label="Single copy orthogroups on ${on_string}">
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter>
+            <change_format>
+                <when input="options_type.create_orthogroup_cond.create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences" value="no" format="ptortho" />
+                <when input="options_type.create_orthogroup_cond.create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences" value="yes" format="ptorthocs" />
+            </change_format>
         </data>
         <data name="output_single_copy" format="tabular" label="Single copy orthogroups on ${on_string}">
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'no' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter>