Mercurial > repos > greg > gene_family_classifier
comparison gene_family_classifier.xml @ 52:921804e9ec8c draft
Uploaded
author | greg |
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date | Wed, 08 Feb 2017 15:00:25 -0500 |
parents | 3b2d35b75268 |
children | 1b776f5fd60a |
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51:3b2d35b75268 | 52:921804e9ec8c |
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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> |