comparison gene_family_classifier.xml @ 88:aef4df6e8ee0 draft

Uploaded
author greg
date Thu, 23 Feb 2017 14:38:57 -0500
parents 2cb2c3349c57
children 81d1832bc0dc
comparison
equal deleted inserted replaced
87:2cb2c3349c57 88:aef4df6e8ee0
114 #if $create_corresponding_coding_sequences: 114 #if $create_corresponding_coding_sequences:
115 #set out_file = $output_ptorthocs 115 #set out_file = $output_ptorthocs
116 #else: 116 #else:
117 #set out_file = $output_ptortho 117 #set out_file = $output_ptortho
118 #end if 118 #end if
119 && echo -e '<html>\n<head>\n<title>Galaxy - GeneFamilyClassifier Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' > $out_file 119 && echo -e "<html>\n<head>\n<title>Galaxy - GeneFamilyClassifier Output</title>\n</head>\n<body>\n<p/>\n<ul>\n" > $out_file
120 #for $fname in $os.listdir($orthogroups_fasta_src_dir): 120 #for $fname in $os.listdir($orthogroups_fasta_src_dir):
121 && echo -e '<li><a href="$fname">$fname</a></li>\n' >> $out_file 121 && echo -e "<li><a href=\"$fname\">$fname</a></li>\n" >> $out_file
122 #end for 122 #end for
123 && echo -e '</ul>\n</body>\n</html>\n' >> $out_file 123 && echo -e "</ul>\n</body>\n</html>\n" >> $out_file
124 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir || true 124 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir || true
125 #end if 125 #end if
126 126
127 #if $single_copy_orthogroup: 127 #if $single_copy_orthogroup:
128 #if $create_ortho_sequences: 128 #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 129 && echo -e "<html>\n<head>\n<title>Galaxy - GeneFamilyClassifier Output</title>\n</head>\n<body>\n<p/>\n<ul>\n" > $output_ptsco
130 #for $fname in $os.listdir($single_copy_fasta_src_dir): 130 #for $fname in $os.listdir($single_copy_fasta_src_dir):
131 && echo -e '<li><a href="$fname">$fname</a></li>\n' >> $output_ptsco 131 && echo -e "<li><a href=\"$fname\">$fname</a></li>\n" >> $output_ptsco
132 #end for 132 #end for
133 && echo -e '</ul>\n</body>\n</html>\n' >> $output_ptsco 133 && echo -e "</ul>\n</body>\n</html>\n" >> $output_ptsco
134 && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir || true 134 && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir || true
135 #end if 135 #end if
136 #end if 136 #end if
137 ]]> 137 ]]>
138 </command> 138 </command>