# 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 @@
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'
-
+
options_type['options_type_selector'] == 'advanced' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'
@@ -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?".