# HG changeset patch
# User greg
# Date 1486663472 18000
# Node ID 774c1ad296e713e5706e295278387e1e1774dede
# Parent  c96583b389a7bdc49caa36735f945e69075dec51
Uploaded

diff -r c96583b389a7 -r 774c1ad296e7 gene_family_classifier.xml
--- a/gene_family_classifier.xml	Thu Feb 09 12:42:10 2017 -0500
+++ b/gene_family_classifier.xml	Thu Feb 09 13:04:32 2017 -0500
@@ -106,16 +106,19 @@
 
             #if $create_ortho_sequences:
                 #if $create_corresponding_coding_sequences:
-                    && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptorthocs
+                    && echo "#Size\tName" > $output_ptorthocs
+                    && 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_ptortho
+                    && echo "#Size\tName" > $output_ptortho
+                    && 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
 
             #if $single_copy_orthogroup:
                 #if $create_ortho_sequences:
-                    && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptsco
+                    && echo "#Size\tName" > $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
                 #end if
             #end if
@@ -188,12 +191,12 @@
                                 optional parameter for the hard-coded path to the config.
                                 <option value="custom" selected="true">Single copy orthogroup custom</option>
                                 -->
-                                <option value="taxa">Minumum single copy taxa required in orthogroup</option>
+                                <option value="taxa">Minimum single copy taxa required in orthogroup</option>
                             </param>
                             <when value="custom" />
                             <when value="taxa">
-                                <param name="single_copy_taxa" type="integer" value="20" label="Minumum single copy taxa required in orthogroup"/>
-                                <param name="taxa_present" type="integer" value="21" label="Minumum taxa required in single copy orthogroup"/>
+                                <param name="single_copy_taxa" type="integer" value="20" label="Minimum single copy taxa required in orthogroup"/>
+                                <param name="taxa_present" type="integer" value="21" label="Minimum taxa required in single copy orthogroup"/>
                             </when>
                         </conditional>
                     </when>
@@ -279,9 +282,9 @@
  * **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.
+ * **Specify single copy orthogroup selection?** - Select 'Yes' to specify 'Minimum single copy taxa required in orthogroup'.
+ * **Minimum single copy taxa required in orthogroup** - Used with "Minimum single copy taxa required in orthogroup" configuration only.
+ * **Minimum taxa required in single copy orthogroup** - Used with "Minimum single copy taxa required in orthogroup" configuration only.
  * **Corresponding coding sequences (CDS) fasta file** - Used only when selecting "Create orthogroup fasta files?".
  
     </help>