Mercurial > repos > bgruening > repeat_masker

comparison RepeatMasker.xml @ 1:880265000696 draft

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Uploaded
author bgruening
date Tue, 25 Jun 2013 08:58:21 -0400
parents d4a2c739da3f
children 5673e72241aa
comparison
equal deleted inserted replaced
0:d4a2c739da3f 1:880265000696
64 #if $adv_opts.adv_opts_selector=="advanced": 64 #if $adv_opts.adv_opts_selector=="advanced":
65 65
66 #if "summary" in $output_files_list: 66 #if "summary" in $output_files_list:
67 ## Write out the summary file (default) 67 ## Write out the summary file (default)
68 #set $summary_file = $output_basename + '.tbl' 68 #set $summary_file = $output_basename + '.tbl'
69 touch $summary_file 69 touch $summary_file;
70 cp $summary_file $output_summary; 70 cp $summary_file $output_summary;
71 #end if 71 #end if
72 72
73 #if "gff" in $output_files_list: 73 #if "gff" in $output_files_list:
74 ## Write out the gff file (default) 74 ## Write out the gff file (default)
75 #set $gff_file = $output_basename + '.out.gff' 75 #set $gff_file = $output_basename + '.out.gff'
76 touch $gff_file 76 touch $gff_file;
77 cp $gff_file $output_gff; 77 cp $gff_file $output_gff;
78 #end if 78 #end if
79 79
80 #if "html" in $output_files_list: 80 #if "html" in $output_files_list:
81 ## Write out the html file 81 ## Write out the html file
82 #set $html_file = $output_basename + '.out.html' 82 #set $html_file = $output_basename + '.out.html'
83 touch $html_file 83 touch $html_file;
84 cp $html_file $output_html; 84 cp $html_file $output_html;
85 #end if 85 #end if
86 86
87 #else: 87 #else:
88 88
89 ## Write out the summary file (default) 89 ## Write out the summary file (default)
90 #set $summary_file = $output_basename + '.tbl' 90 #set $summary_file = $output_basename + '.tbl'
91 touch $summary_file 91 touch $summary_file;
92 cp $summary_file $output_summary; 92 cp $summary_file $output_summary;
93 93
94 ## Write out the gff file (default) 94 ## Write out the gff file (default)
95 #set $gff_file = $output_basename + '.out.gff' 95 #set $gff_file = $output_basename + '.out.gff'
96 touch $gff_file 96 touch $gff_file;
97 cp $gff_file $output_gff; 97 cp $gff_file $output_gff;
98 98
99 99
100 ## End of advanced options: 100 ## End of advanced options:
101 #end if 101 #end if
102 102
103 ## Write out mask sequence file 103 ## Write out mask sequence file
104 #set $mask_sequence_file = $output_basename + '.masked' 104 #set $mask_sequence_file = $output_basename + '.masked'
105 touch $mask_sequence_file 105 touch $mask_sequence_file;
106 cp $mask_sequence_file $output_mask; 106 cp $mask_sequence_file $output_mask;
107 107
108 ## Write out standard file (default) 108 ## Write out standard file (default)
109 ## The default '.out' file from RepeatMasker has a 3-line header and spaces rather 109 ## The default '.out' file from RepeatMasker has a 3-line header and spaces rather
110 ## than tabs. Remove the header and replace the whitespaces with tab 110 ## than tabs. Remove the header and replace the whitespaces with tab