Mercurial > repos > greg > gene_family_classifier
changeset 45:916fb0014f89 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 07 Feb 2017 13:40:58 -0500 |
| parents | 46f43a90492a |
| children | 6c3fa9907d9c |
| files | gene_family_classifier.xml |
| diffstat | 1 files changed, 7 insertions(+), 11 deletions(-) [+] |
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--- 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?".