# HG changeset patch # User greg # Date 1491935063 14400 # Node ID b2ae23e484e80b482db1518ff800456c389a6998 # Parent 169504db8e43a7891d8a919d3dc1feded0b479d5 Uploaded diff -r 169504db8e43 -r b2ae23e484e8 gene_family_classifier.py --- a/gene_family_classifier.py Fri Apr 07 08:38:49 2017 -0400 +++ b/gene_family_classifier.py Tue Apr 11 14:24:23 2017 -0400 @@ -12,15 +12,15 @@ parser = argparse.ArgumentParser() parser.add_argument('--input', dest='input', help="Input dataset") -parser.add_argument('--scaffold', dest='scaffold', default='mode', help='Orthogroups or gene families proteins scaffold') +parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold') parser.add_argument('--method', dest='method', help='Protein clustering method') parser.add_argument('--classifier', dest='classifier', help='Protein classification method') parser.add_argument('--config_dir', dest='config_dir', help='Directory containing default configuration files') parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution') parser.add_argument('--super_orthogroups', dest='super_orthogroups', default=None, help='Super orthogroups clustering specification') parser.add_argument('--single_copy_custom', dest='single_copy_custom', default=None, help='Custom single copy orthogroup configuration') -parser.add_argument('--single_copy_taxa', dest='single_copy_taxa', type=int, default=None, help='"Minimum single copy taxa required in orthogroup') -parser.add_argument('--taxa_present', dest='taxa_present', type=int, default=None, help='Minimum taxa required in single copy orthogroup') +parser.add_argument('--single_copy_taxa', dest='single_copy_taxa', type=int, default=0, help='"Minimum single copy taxa required in orthogroup') +parser.add_argument('--taxa_present', dest='taxa_present', type=int, default=0, help='Minimum taxa required in single copy orthogroup') parser.add_argument('--orthogroup_fasta', dest='orthogroup_fasta', default=None, help='Flag to create orthogroup sequences') parser.add_argument('--coding_sequences', dest='coding_sequences', default=None, help='Flag to create orthogroup coding sequences') parser.add_argument('--save_hmmscan_log', dest='save_hmmscan_log', default=None, help='Flag to save the hmmscan log') @@ -47,9 +47,9 @@ cmd += ' --super_orthogroups %s' % args.super_orthogroups if args.single_copy_custom is not None: cmd += ' --single_copy_custom %s' % args.single_copy_custom -if args.single_copy_taxa is not None: +if args.single_copy_taxa > 0: cmd += ' --single_copy_taxa %d' % args.single_copy_taxa -if args.taxa_present is not None: +if args.taxa_present > 0: cmd += ' --taxa_present %d' % args.taxa_present if args.orthogroup_fasta is None: create_ortho_sequences = False diff -r 169504db8e43 -r b2ae23e484e8 gene_family_classifier.xml --- a/gene_family_classifier.xml Fri Apr 07 08:38:49 2017 -0400 +++ b/gene_family_classifier.xml Tue Apr 11 14:24:23 2017 -0400 @@ -1,4 +1,4 @@ - + classifies gene sequences into pre-computed orthologous plant gene family clusters macros.xml @@ -67,10 +67,10 @@ --single_copy_custom '$single_copy_custom_cond.single_copy_custom_config' #end if #else: - #if $single_copy_cond.single_copy_taxa > 0: + #if str($single_copy_cond.single_copy_taxa): --single_copy_taxa $single_copy_cond.single_copy_taxa #end if - #if $single_copy_cond.taxa_present > 0: + #if str($single_copy_cond.taxa_present): --taxa_present $single_copy_cond.taxa_present #end if #end if @@ -180,8 +180,8 @@ - - + + @@ -272,7 +272,7 @@ * **Selection criterion** - single/low-copy orthogroups selection criterion. PlantTribes provides custom and global selection criteria for selecting user-defined single/low-copy scaffold orthogoups. - * **Global selection configuration** - the upper limit values of the following two parameters vary depending on the selected gene family scaffold, and the tool will produce an error if the value exceeds the number of species in the circumscribed scaffold. Zero values have no affect. + * **Global selection configuration** - the upper limit values of the following two parameters vary depending on the selected gene family scaffold, and the tool will produce an error if the value exceeds the number of species in the circumscribed scaffold. * **Minimum single copy taxa** - minimum number of taxa with single copy genes in the orthogroup. * **Minimum taxa present** - minimum number of taxa present in the orthogroup. diff -r 169504db8e43 -r b2ae23e484e8 macros.xml --- a/macros.xml Fri Apr 07 08:38:49 2017 -0400 +++ b/macros.xml Tue Apr 11 14:24:23 2017 -0400 @@ -1,10 +1,16 @@ + 0.8 plant_tribes_assembly_post_processor + + + plant_tribes_gene_family_aligner + + plant_tribes_gene_family_classifier @@ -15,6 +21,16 @@ plant_tribes_gene_family_integrator + + + plant_tribes_kaks_analysis + + + + + plant_tribes_gene_family_phylogeny_builder + + @@ -23,10 +39,10 @@ - - - - + + + + @@ -36,12 +52,74 @@ + + + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @misc{None,