Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 37:36f85b2570be draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Thu, 02 Feb 2017 11:03:04 -0500
parents d485da50616b
children b63f96ff6708
comparison
equal deleted inserted replaced
36:d485da50616b 37:36f85b2570be
31 #end if 31 #end if
32 32
33 #set create_ortho_sequences = True 33 #set create_ortho_sequences = True
34 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta') 34 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
35 #if $create_corresponding_coding_sequences: 35 #if $create_corresponding_coding_sequences:
36 #set dest_dir = $output_pgfccs.extra_files_path 36 #set dest_dir = $output_ptefccs.extra_files_path
37 #else: 37 #else:
38 #set dest_dir = $output_pgfc.extra_files_path 38 #set dest_dir = $output_ptefc.extra_files_path
39 #end if 39 #end if
40 mkdir -p $dest_dir && 40 mkdir -p $dest_dir &&
41 #else: 41 #else:
42 #set create_ortho_sequences = False 42 #set create_ortho_sequences = False
43 #set create_corresponding_coding_sequences = False 43 #set create_corresponding_coding_sequences = False
77 #end if 77 #end if
78 #end if 78 #end if
79 79
80 #if $create_ortho_sequences: 80 #if $create_ortho_sequences:
81 #if $create_corresponding_coding_sequences: 81 #if $create_corresponding_coding_sequences:
82 && echo "# Precomputed orthologous gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_pgfccs 82 && echo "# Precomputed orthologous gene family clusters with corresponding coding sequences: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_ptefccs
83 && ls -al $orthogroups_fasta_src_dir | grep f >> $output_pgfccs 83 && ls -al $orthogroups_fasta_src_dir | grep f >> $output_ptefccs
84 #else: 84 #else:
85 && echo "# Precomputed orthologous gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_pgfc 85 && echo "# Precomputed orthologous gene family clusters: `ls $orthogroups_fasta_src_dir | grep f | wc -l` files" > $output_ptefc
86 && ls -al $orthogroups_fasta_src_dir | grep f >> $output_pgfc 86 && ls -al $orthogroups_fasta_src_dir | grep f >> $output_ptefc
87 #end if 87 #end if
88 && mv $orthogroups_fasta_src_dir/* $dest_dir || true 88 && mv $orthogroups_fasta_src_dir/* $dest_dir || true
89 #end if 89 #end if
90 90
91 ]]> 91 ]]>
167 </inputs> 167 </inputs>
168 <outputs> 168 <outputs>
169 <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}"> 169 <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}">
170 <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter> 170 <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter>
171 </data> 171 </data>
172 <data name="output_pgfc" format="pgfc" label="Gene family clusters on ${on_string}"> 172 <data name="output_ptefc" format="ptefc" label="Gene family clusters on ${on_string}">
173 <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> 173 <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>
174 </data> 174 </data>
175 <data name="output_pgfccs" format="pgfccs" label="Gene family clusters and corresponding coding sequences on ${on_string}"> 175 <data name="output_ptefccs" format="ptefccs" label="Gene family clusters and corresponding coding sequences on ${on_string}">
176 <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> 176 <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>
177 </data> 177 </data>
178 <collection name="orthos" type="list"> 178 <collection name="orthos" type="list">
179 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" /> 179 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
180 </collection> 180 </collection>