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comparison flexbar.xml @ 12:4cbf6c6d2f2b

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Fixed issue where adapter removal can not be performed and further minor issues.
author jtilman
date Thu, 17 Jan 2013 18:09:44 +0100
parents 589b4866f537
children 346a2b0979ea
comparison
equal deleted inserted replaced
11:52c5e53aff28 12:4cbf6c6d2f2b
92 #if $cBarcodes.cbAlignScores.select == "yes": 92 #if $cBarcodes.cbAlignScores.select == "yes":
93 --barcode-match $bMatch 93 --barcode-match $bMatch
94 --barcode-mismatch $bMismatch 94 --barcode-mismatch $bMismatch
95 --barcode-gap $bGap 95 --barcode-gap $bGap
96 #end if 96 #end if
97 97 #end if
98 #end if 98
99 99
100 100 #if $cAdapters.select == "on":
101 #if $cAdapters.select == "yes":
102 101
103 #if $cAdapters.ccAdapters.select == "data": 102 #if $cAdapters.ccAdapters.select == "data":
104 --adapters $cAdapters.ccAdapters.adaptersData 103 --adapters $cAdapters.ccAdapters.adaptersData
105 #end if 104 #end if
106 105
115 #end if 114 #end if
116 115
117 --adapter-min-overlap $cAdapters.aMinOverlap 116 --adapter-min-overlap $cAdapters.aMinOverlap
118 --adapter-threshold $cAdapters.aThresh 117 --adapter-threshold $cAdapters.aThresh
119 118
120 #if $cAdapters.caAlignScores.select == "on": 119 #if $cAdapters.caAlignScores.select == "yes":
121 --adapter-match $aMatch 120 --adapter-match $aMatch
122 --adapter-mismatch $aMismatch 121 --adapter-mismatch $aMismatch
123 --adapter-gap $aGap 122 --adapter-gap $aGap
124 #end if 123 #end if
125 124 #end if
126 #end if 125
127 126
128 127 #if $cLogging.select == "show":
129 #if $cLogging.select == "show"
130 $cLogging.logLevel 128 $cLogging.logLevel
131 $cLogging.noLenDist 129 $cLogging.noLenDist
132 $cLogging.remTag 130 $cLogging.remTag
133 #end if 131 #end if
134 132
135 #if $cLogging.select == "off" 133 #if $cLogging.select == "off":
136 --no-length-dist 134 --no-length-dist
137 #end if 135 #end if
138 136
139 137
140 $output $output.id $__new_file_path__ $reads.ext 138 $output $output.id $__new_file_path__ $reads.ext