Mercurial > repos > greg > gene_family_classifier
changeset 63:dd22169524ee draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 09 Feb 2017 11:29:23 -0500 |
| parents | ffaedadf9c18 |
| children | c96583b389a7 |
| files | gene_family_classifier.xml |
| diffstat | 1 files changed, 11 insertions(+), 7 deletions(-) [+] |
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--- a/gene_family_classifier.xml Thu Feb 09 10:53:31 2017 -0500 +++ b/gene_family_classifier.xml Thu Feb 09 11:29:23 2017 -0500 @@ -41,10 +41,10 @@ #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 + #set orthogroups_fasta_dest_dir = $output_ptorthocs.extra_files_path #else: #set create_corresponding_coding_sequences = False - #set orthogroups_fasta_dest_dir = $output_ptcgf.extra_files_path + #set orthogroups_fasta_dest_dir = $output_ptortho.extra_files_path #end if mkdir -p $orthogroups_fasta_dest_dir && #else: @@ -107,9 +107,9 @@ #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_ptorthocs #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_ptortho #end if && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir #end if @@ -227,14 +227,18 @@ <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}"> <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter> </data> - <data name="output_ptcgf" format="ptcgf" label="Gene family clusters on ${on_string}"> + <data name="output_ptortho" format="ptortho" label="Gene family clusters 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'] == 'no'</filter> </data> - <data name="output_ptcgfcs" format="ptcgfcs" label="Gene family clusters and corresponding coding sequences on ${on_string}"> + <data name="output_ptorthocs" format="ptorthocs" 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="txt" label="Single copy orthogroups on ${on_string}"> + <data name="output_ptsco" format="tabular" label="Single copy orthogroups on ${on_string}"> <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter> + <change_format> + <when input="options_type.create_orthogroup_cond.create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences" value="no" format="ptortho" /> + <when input="options_type.create_orthogroup_cond.create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences" value="yes" format="ptorthocs" /> + </change_format> </data> <data name="output_single_copy" format="tabular" label="Single copy orthogroups on ${on_string}"> <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'no' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter>