comparison gene_family_classifier.xml @ 52:921804e9ec8c draft

Uploaded
author greg
date Wed, 08 Feb 2017 15:00:25 -0500
parents 3b2d35b75268
children 1b776f5fd60a
comparison
equal deleted inserted replaced
51:3b2d35b75268 52:921804e9ec8c
31 #set super_orthogroups = $specify_super_orthogroups_cond.super_orthogroups 31 #set super_orthogroups = $specify_super_orthogroups_cond.super_orthogroups
32 #else: 32 #else:
33 #set specify_super_orthos = False 33 #set specify_super_orthos = False
34 #end if 34 #end if
35 35
36 #if str($specify_single_copy) == 'yes':
37 #set single_copy_orthogroup = True
38 #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta')
39 #set single_copy_fasta_dest_dir = $output_ptsco.extra_files_path
40 #set single_copy_cond = $specify_single_copy_cond.single_copy_cond
41 ## FixMe: the single_copy_custom option is not currently supported.
42 #set single_copy = $single_copy_cond.single_copy
43 mkdir -p $single_copy_fasta_dest_dir &&
44 #else:
45 #set single_copy_orthogroup = False
46 #end if
47
48 #if str($create_orthogroup) == 'yes': 36 #if str($create_orthogroup) == 'yes':
49 #set create_ortho_sequences = True 37 #set create_ortho_sequences = True
50 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta') 38 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
51 #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond 39 #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond
52 40
60 mkdir -p $orthogroups_fasta_dest_dir && 48 mkdir -p $orthogroups_fasta_dest_dir &&
61 #else: 49 #else:
62 #set create_ortho_sequences = False 50 #set create_ortho_sequences = False
63 #set create_corresponding_coding_sequences = False 51 #set create_corresponding_coding_sequences = False
64 #end if 52 #end if
53
54 #if str($specify_single_copy) == 'yes':
55 #set single_copy_orthogroup = True
56 #set single_copy_cond = $specify_single_copy_cond.single_copy_cond
57 ## FixMe: the single_copy_custom option is not currently supported.
58 #set single_copy = $single_copy_cond.single_copy
59 #if $create_ortho_sequences:
60 #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta')
61 #set single_copy_fasta_dest_dir = $output_ptsco.extra_files_path
62 mkdir -p $single_copy_fasta_dest_dir &&
63 #end if:
64 #else:
65 #set single_copy_orthogroup = False
66 #end if
67
65 #else: 68 #else:
66 #set single_copy_orthogroup = False 69 #set single_copy_orthogroup = False
67 #set create_ortho_sequences = False 70 #set create_ortho_sequences = False
68 #set create_corresponding_coding_sequences = False 71 #set create_corresponding_coding_sequences = False
69 #end if 72 #end if
99 #else: 102 #else:
100 && rm geneFamilyClassification_dir/hmmscan.log 103 && rm geneFamilyClassification_dir/hmmscan.log
101 #end if 104 #end if
102 #end if 105 #end if
103 106
104 #if $create_ortho_sequences: 107 #if $create_ortho_sequences and $os.path.exists($orthogroups_fasta_src_dir) and len($os.listdir($orthogroups_fasta_src_dir)) > 0:
105 #if $create_corresponding_coding_sequences: 108 #if $create_corresponding_coding_sequences:
106 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgfcs 109 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgfcs
107 #else: 110 #else:
108 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgf 111 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgf
109 #end if 112 #end if
110 #if $os.path.exists($orthogroups_fasta_src_dir) and len($os.listdir($orthogroups_fasta_src_dir)) > 0: 113 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir
111 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir
112 #end if
113 #end if 114 #end if
114 115
115 #if $single_copy_orthogroup: 116 #if $single_copy_orthogroup:
116 && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptsco 117 #if $create_ortho_sequences and $os.path.exists($single_copy_fasta_src_dir) and len($os.listdir($single_copy_fasta_src_dir)) > 0:
117 #if $os.path.exists($single_copy_fasta_src_dir) and len($os.listdir($single_copy_fasta_src_dir)) > 0: 118 && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptsco
118 && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir 119 && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir
120 #else:
121 && mv geneFamilyClassification_dir/*.singleCopy $output_single_copy
119 #end if 122 #end if
120 #end if 123 #end if
121 ]]> 124 ]]>
122 </command> 125 </command>
123 <inputs> 126 <inputs>
228 </data> 231 </data>
229 <data name="output_ptcgfcs" format="ptcgfcs" label="Gene family clusters and corresponding coding sequences on ${on_string}"> 232 <data name="output_ptcgfcs" format="ptcgfcs" label="Gene family clusters and corresponding coding sequences on ${on_string}">
230 <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> 233 <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>
231 </data> 234 </data>
232 <data name="output_ptsco" format="txt" label="Single copy orthogroup on ${on_string}"> 235 <data name="output_ptsco" format="txt" label="Single copy orthogroup on ${on_string}">
233 <filter>options_type['options_type_selector'] == 'advanced' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter> 236 <filter>options_type['options_type_selector'] == 'advanced' and and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter>
237 </data>
238 <data name="output_single_copy" format="tabular" label="Single copy orthogroup on ${on_string}">
239 <filter>options_type['options_type_selector'] == 'advanced' and and options_type['create_orthogroup_cond']['create_orthogroup'] == 'no' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter>
234 </data> 240 </data>
235 <collection name="orthos" type="list"> 241 <collection name="orthos" type="list">
236 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" /> 242 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
237 </collection> 243 </collection>
238 </outputs> 244 </outputs>