# HG changeset patch
# User greg
# Date 1486492858 18000
# Node ID 916fb0014f899b240804087aeea7e85779d388e5
# Parent  46f43a90492a60c62f5e91aa9398c63c0118cba7
Uploaded

diff -r 46f43a90492a -r 916fb0014f89 gene_family_classifier.xml
--- a/gene_family_classifier.xml	Tue Feb 07 11:48:18 2017 -0500
+++ b/gene_family_classifier.xml	Tue Feb 07 13:40:58 2017 -0500
@@ -31,7 +31,6 @@
                     #set single_copy_cond = $specify_single_copy_cond.single_copy_cond
                     ## FixMe: the single_copy_custom option is not currently supported.
                     #set single_copy = $single_copy_cond.single_copy
-
                     mkdir -p $single_copy_fasta_dest_dir &&
                 #else:
                     #set specify_single_copy = False
@@ -44,22 +43,18 @@
 
                     #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
                     #else:
                         #set create_corresponding_coding_sequences = False
-                    #end if
-
-                    #if $create_corresponding_coding_sequences:
-                        #set orthogroups_fasta_dest_dir = $output_ptcgfcs.extra_files_path
-                    #else:
                         #set orthogroups_fasta_dest_dir = $output_ptcgf.extra_files_path
                     #end if
-
                     mkdir -p $orthogroups_fasta_dest_dir &&
                 #else:
                     #set create_ortho_sequences = False
                     #set create_corresponding_coding_sequences = False
                 #end if
             #else:
+                #set specify_single_copy = False
                 #set create_ortho_sequences = False
                 #set create_corresponding_coding_sequences = False
             #end if
@@ -97,15 +92,15 @@
 
             #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_ptcgfcs
                 #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_ptcgf
                 #end if
                 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir || true
             #end if
 
             #if $specify_single_copy:
-                && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptsco
+                && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptsco
                 && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir || true
             #end if
         ]]>
@@ -210,7 +205,7 @@
         <data name="output_ptcgfcs" format="ptcgfcs" 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="ptsco" label="Single copy orthogroup on ${on_string}">
+        <data name="output_ptsco" format="txt" label="Single copy orthogroup on ${on_string}">
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter>
         </data>
         <collection name="orthos" type="list">
@@ -255,6 +250,7 @@
  * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
  * **Protein classification method** - blastp (faster), HMMScan (slower but more sensative to the remote homologs) or both (more exhaustive).
  * **Super Orthogroups** - Secondary MCL clusters of orthogroups.
+ * **Specify single copy orthogroup selection?** - Select 'Yes' to specify one of 'Single copy orthogroup custom' (not yet supported) or 'Minumum single copy taxa required in orthogroup'.
  * **Minumum single copy taxa required in orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only.
  * **Minumum taxa required in single copy orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only.
  * **Corresponding coding sequences (CDS) fasta file** - Used only when selecting "Create orthogroup fasta files?".