Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 63:dd22169524ee draft

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Uploaded
author greg
date Thu, 09 Feb 2017 11:29:23 -0500
parents ffaedadf9c18
children c96583b389a7
comparison
equal deleted inserted replaced
62:ffaedadf9c18 63:dd22169524ee
39 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta') 39 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
40 #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond 40 #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond
41 41
42 #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes': 42 #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes':
43 #set create_corresponding_coding_sequences = True 43 #set create_corresponding_coding_sequences = True
44 #set orthogroups_fasta_dest_dir = $output_ptcgfcs.extra_files_path 44 #set orthogroups_fasta_dest_dir = $output_ptorthocs.extra_files_path
45 #else: 45 #else:
46 #set create_corresponding_coding_sequences = False 46 #set create_corresponding_coding_sequences = False
47 #set orthogroups_fasta_dest_dir = $output_ptcgf.extra_files_path 47 #set orthogroups_fasta_dest_dir = $output_ptortho.extra_files_path
48 #end if 48 #end if
49 mkdir -p $orthogroups_fasta_dest_dir && 49 mkdir -p $orthogroups_fasta_dest_dir &&
50 #else: 50 #else:
51 #set create_ortho_sequences = False 51 #set create_ortho_sequences = False
52 #set create_corresponding_coding_sequences = False 52 #set create_corresponding_coding_sequences = False
105 #end if 105 #end if
106 #end if 106 #end if
107 107
108 #if $create_ortho_sequences: 108 #if $create_ortho_sequences:
109 #if $create_corresponding_coding_sequences: 109 #if $create_corresponding_coding_sequences:
110 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgfcs 110 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptorthocs
111 #else: 111 #else:
112 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgf 112 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptortho
113 #end if 113 #end if
114 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir 114 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir
115 #end if 115 #end if
116 116
117 #if $single_copy_orthogroup: 117 #if $single_copy_orthogroup:
225 </inputs> 225 </inputs>
226 <outputs> 226 <outputs>
227 <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}"> 227 <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}">
228 <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter> 228 <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter>
229 </data> 229 </data>
230 <data name="output_ptcgf" format="ptcgf" label="Gene family clusters on ${on_string}"> 230 <data name="output_ptortho" format="ptortho" label="Gene family clusters on ${on_string}">
231 <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> 231 <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>
232 </data> 232 </data>
233 <data name="output_ptcgfcs" format="ptcgfcs" label="Gene family clusters and corresponding coding sequences on ${on_string}"> 233 <data name="output_ptorthocs" format="ptorthocs" label="Gene family clusters and corresponding coding sequences on ${on_string}">
234 <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> 234 <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>
235 </data> 235 </data>
236 <data name="output_ptsco" format="txt" label="Single copy orthogroups on ${on_string}"> 236 <data name="output_ptsco" format="tabular" label="Single copy orthogroups on ${on_string}">
237 <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> 237 <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>
238 <change_format>
239 <when input="options_type.create_orthogroup_cond.create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences" value="no" format="ptortho" />
240 <when input="options_type.create_orthogroup_cond.create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences" value="yes" format="ptorthocs" />
241 </change_format>
238 </data> 242 </data>
239 <data name="output_single_copy" format="tabular" label="Single copy orthogroups on ${on_string}"> 243 <data name="output_single_copy" format="tabular" label="Single copy orthogroups on ${on_string}">
240 <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> 244 <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>
241 </data> 245 </data>
242 <collection name="orthos" type="list"> 246 <collection name="orthos" type="list">