Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 97:484bedd86474 draft

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Uploaded
author greg
date Mon, 27 Feb 2017 10:48:07 -0500
parents 431a63fced68
children e53492ae4ac0
comparison
equal deleted inserted replaced
96:ba924b724a8d 97:484bedd86474
20 #set specify_super_orthogroups = $specify_super_orthogroups_cond.specify_super_orthogroups 20 #set specify_super_orthogroups = $specify_super_orthogroups_cond.specify_super_orthogroups
21 #set create_orthogroup_cond = $options_type.create_orthogroup_cond 21 #set create_orthogroup_cond = $options_type.create_orthogroup_cond
22 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup 22 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup
23 #set specify_single_copy_cond = $options_type.specify_single_copy_cond 23 #set specify_single_copy_cond = $options_type.specify_single_copy_cond
24 #set specify_single_copy = $specify_single_copy_cond.specify_single_copy 24 #set specify_single_copy = $specify_single_copy_cond.specify_single_copy
25
26 #if str($specify_super_orthogroups) == 'yes': 25 #if str($specify_super_orthogroups) == 'yes':
27 #set specify_super_orthos = True 26 #set specify_super_orthos = True
28 #set super_orthogroups = $specify_super_orthogroups_cond.super_orthogroups 27 #set super_orthogroups = $specify_super_orthogroups_cond.super_orthogroups
29 #else: 28 #else:
30 #set specify_super_orthos = False 29 #set specify_super_orthos = False
31 #end if 30 #end if
32
33 #if str($create_orthogroup) == 'yes': 31 #if str($create_orthogroup) == 'yes':
34 #set create_ortho_sequences = True 32 #set create_ortho_sequences = True
35 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
36 #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond 33 #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond
37
38 #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes': 34 #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes':
39 #set create_corresponding_coding_sequences = True 35 #set create_corresponding_coding_sequences = True
40 #set orthogroups_fasta_dest_dir = $output_ptorthocs.files_path
41 #else: 36 #else:
42 #set create_corresponding_coding_sequences = False 37 #set create_corresponding_coding_sequences = False
43 #set orthogroups_fasta_dest_dir = $output_ptortho.files_path
44 #end if 38 #end if
45 mkdir -p $orthogroups_fasta_dest_dir &&
46 #else: 39 #else:
47 #set create_ortho_sequences = False 40 #set create_ortho_sequences = False
48 #set create_corresponding_coding_sequences = False 41 #set create_corresponding_coding_sequences = False
49 #end if 42 #end if
50
51 #if str($specify_single_copy) == 'yes': 43 #if str($specify_single_copy) == 'yes':
52 #set single_copy_orthogroup = True 44 #set single_copy_orthogroup = True
53 #set single_copy_cond = $specify_single_copy_cond.single_copy_cond 45 #set single_copy_cond = $specify_single_copy_cond.single_copy_cond
54 #set single_copy = $single_copy_cond.single_copy 46 #set single_copy = $single_copy_cond.single_copy
55 #if $create_ortho_sequences:
56 #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta')
57 #set single_copy_fasta_dest_dir = $output_ptsco.files_path
58 mkdir -p $single_copy_fasta_dest_dir &&
59 #end if:
60 #else: 47 #else:
61 #set single_copy_orthogroup = False 48 #set single_copy_orthogroup = False
62 #end if 49 #end if
63
64 #else: 50 #else:
65 #set single_copy_orthogroup = False 51 #set single_copy_orthogroup = False
66 #set create_ortho_sequences = False 52 #set create_ortho_sequences = False
67 #set create_corresponding_coding_sequences = False 53 #set create_corresponding_coding_sequences = False
68 #end if 54 #end if
98 #if $create_corresponding_coding_sequences: 84 #if $create_corresponding_coding_sequences:
99 --coding_sequences '$create_corresponding_coding_sequences_cond.coding_sequences' 85 --coding_sequences '$create_corresponding_coding_sequences_cond.coding_sequences'
100 #end if 86 #end if
101 #end if 87 #end if
102 #end if 88 #end if
103 >/dev/null 89
104 90 #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both' and str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes':
105 #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both': 91 --save_hmmscan_log
106 #if str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes': 92 --hmmscan_log '$hmmscan_log'
107 && mv geneFamilyClassification_dir/hmmscan.log $hmmscan_log 93 #end if
108 #else:
109 && rm geneFamilyClassification_dir/hmmscan.log
110 #end if
111 #end if
112
113 #if $create_ortho_sequences: 94 #if $create_ortho_sequences:
114 #if $create_corresponding_coding_sequences: 95 #if $create_corresponding_coding_sequences:
115 #set out_file = $output_ptorthocs 96 --output_ptorthocs '$output_ptorthocs'
116 #else: 97 #else:
117 #set out_file = $output_ptortho 98 --output_ptortho '$output_ptortho'
118 #end if 99 #end if
119 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir || true 100 #end if
120 && echo -e "<html>\n<head>\n<title>orthogroups</title>\n</head>\n<body>\n<p/>\n<ul>\n" > $out_file
121 && for f in "$orthogroups_fasta_dest_dir"/*; do if [ -f "$f" ]; then echo -e "<li><a href=\"$f\">$f</a></li>\n" >> $out_file; fi; done
122 && echo -e "</ul>\n</body>\n</html>\n" >> $out_file
123 #end if
124
125 #if $single_copy_orthogroup: 101 #if $single_copy_orthogroup:
126 #if $create_ortho_sequences: 102 #if $create_ortho_sequences:
127 && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir || true 103 --output_ptsco '$output_ptsco'
128 && echo -e "<html>\n<head>\n<title>single copy orthogroups</title>\n</head>\n<body>\n<p/>\n<ul>\n" > $output_ptsco
129 && for f in "$single_copy_fasta_dest_dir"/*; do if [ -f "$f" ]; then echo -e "<li><a href=\"$f\">$f</a></li>\n" >> $output_ptsco; fi; done
130 && echo -e "</ul>\n</body>\n</html>\n" >> $output_ptsco
131 #end if 104 #end if
132 #end if 105 #end if
133 ]]> 106 ]]>
134 </command> 107 </command>
135 <inputs> 108 <inputs>
175 <option value="no" selected="true">No</option> 148 <option value="no" selected="true">No</option>
176 <option value="yes">Yes</option> 149 <option value="yes">Yes</option>
177 </param> 150 </param>
178 <when value="no"/> 151 <when value="no"/>
179 <when value="yes"> 152 <when value="yes">
180 <param name="super_orthogroups" type="select" label="Super Orthogroups"> 153 <param name="super_orthogroups" type="select" label="Super orthogroups clustering specification">
181 <option value="min_evalue" selected="true">Minimum e-value</option> 154 <option value="min_evalue" selected="true">Minimum e-value</option>
182 <option value="avg_evalue">Average e-value</option> 155 <option value="avg_evalue">Average e-value</option>
183 </param> 156 </param>
184 </when> 157 </when>
185 </conditional> 158 </conditional>