Mercurial > repos > greg > gene_family_classifier
changeset 65:774c1ad296e7 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 09 Feb 2017 13:04:32 -0500 |
| parents | c96583b389a7 |
| children | 7525307aa1d7 |
| files | gene_family_classifier.xml |
| diffstat | 1 files changed, 12 insertions(+), 9 deletions(-) [+] |
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--- 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>