Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 86:9548303eec2f draft

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Uploaded
author greg
date Thu, 23 Feb 2017 09:44:09 -0500
parents 97f9b65d8e44
children 2cb2c3349c57
comparison
equal deleted inserted replaced
85:97f9b65d8e44 86:9548303eec2f
35 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta') 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 36 #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond
37 37
38 #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes': 38 #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes':
39 #set create_corresponding_coding_sequences = True 39 #set create_corresponding_coding_sequences = True
40 #set orthogroups_fasta_dest_dir = $output_ptorthocs.files_path 40 #set orthogroups_fasta_dest_dir = $output_ptorthocs.extra_files_path
41 #else: 41 #else:
42 #set create_corresponding_coding_sequences = False 42 #set create_corresponding_coding_sequences = False
43 #set orthogroups_fasta_dest_dir = $output_ptortho.files_path 43 #set orthogroups_fasta_dest_dir = $output_ptortho.extra_files_path
44 #end if 44 #end if
45 mkdir -p $orthogroups_fasta_dest_dir && 45 mkdir -p $orthogroups_fasta_dest_dir &&
46 #else: 46 #else:
47 #set create_ortho_sequences = False 47 #set create_ortho_sequences = False
48 #set create_corresponding_coding_sequences = False 48 #set create_corresponding_coding_sequences = False
52 #set single_copy_orthogroup = True 52 #set single_copy_orthogroup = True
53 #set single_copy_cond = $specify_single_copy_cond.single_copy_cond 53 #set single_copy_cond = $specify_single_copy_cond.single_copy_cond
54 #set single_copy = $single_copy_cond.single_copy 54 #set single_copy = $single_copy_cond.single_copy
55 #if $create_ortho_sequences: 55 #if $create_ortho_sequences:
56 #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta') 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 57 #set single_copy_fasta_dest_dir = $output_ptsco.extra_files_path
58 mkdir -p $single_copy_fasta_dest_dir && 58 mkdir -p $single_copy_fasta_dest_dir &&
59 #end if: 59 #end if:
60 #else: 60 #else:
61 #set single_copy_orthogroup = False 61 #set single_copy_orthogroup = False
62 #end if 62 #end if
110 #end if 110 #end if
111 #end if 111 #end if
112 112
113 #if $create_ortho_sequences: 113 #if $create_ortho_sequences:
114 #if $create_corresponding_coding_sequences: 114 #if $create_corresponding_coding_sequences:
115 #set out_file = $output_ptorthocs 115 && echo -e "#Size\tName" > $output_ptorthocs
116 #else: 116 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptorthocs
117 #set out_file = $output_ptortho 117 #else:
118 #end if 118 && echo -e "#Size\tName" > $output_ptortho
119 && echo -e '<html>\n<head>\n<title>Galaxy - GeneFamilyClassifier Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' > $out_file 119 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptortho
120 #for $fname in $os.listdir($orthogroups_fasta_src_dir): 120 #end if
121 && echo -e '<li><a href="$fname">$fname</a></li>\n' >> $out_file
122 #end for
123 && echo -e '</ul>\n</body>\n</html>\n' >> $out_file
124 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir || true 121 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir || true
125 #end if 122 #end if
126 123
127 #if $single_copy_orthogroup: 124 #if $single_copy_orthogroup:
128 #if $create_ortho_sequences: 125 #if $create_ortho_sequences:
129 && echo -e '<html>\n<head>\n<title>Galaxy - GeneFamilyClassifier Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' > $output_ptsco 126 && echo -e "#Size\tName" > $output_ptsco
130 #for $fname in $os.listdir($single_copy_fasta_src_dir): 127 && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_ptsco
131 && echo -e '<li><a href="$fname">$fname</a></li>\n' >> $output_ptsco
132 #end for
133 && echo -e '</ul>\n</body>\n</html>\n' >> $output_ptsco
134 && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir || true 128 && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir || true
135 #end if 129 #end if
136 #end if 130 #end if
137 ]]> 131 ]]>
138 </command> 132 </command>