Mercurial > repos > blankenberg > naive_variant_caller

comparison tools/naive_variant_caller.xml @ 8:d5f866df45ae

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author blankenberg
date Thu, 29 Jan 2015 15:02:01 -0500
parents 8398666758e3
children 4fab5fce1adb
comparison
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7:3c3ef33b9d56 8:d5f866df45ae
44 #end if 44 #end if
45 45
46 --allow_out_of_bounds_positions 46 --allow_out_of_bounds_positions
47 47
48 #if str( $advanced_options.advanced_options_selector ) == "advanced": 48 #if str( $advanced_options.advanced_options_selector ) == "advanced":
49 --coverage_dtype "${advanced_options.coverage_dtype}" 49 #if str( $advanced_options.coverage_dtype ) != "guess":
50 --coverage_dtype "${advanced_options.coverage_dtype}"
51 #end if
50 ${advanced_options.safe} 52 ${advanced_options.safe}
51 #else
52 --coverage_dtype "uint64"
53 #end if 53 #end if
54 </command> 54 </command>
55 <inputs> 55 <inputs>
56 <conditional name="reference_source"> 56 <conditional name="reference_source">
57 <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> 57 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
105 <when value="basic"> 105 <when value="basic">
106 <!-- Do nothing here --> 106 <!-- Do nothing here -->
107 </when> 107 </when>
108 <when value="advanced"> 108 <when value="advanced">
109 <param name="coverage_dtype" type="select" label="Choose the dtype to use for storing coverage information" help="This affects the maximum recorded value for a position, e.g. uint8 would be 255 coverage, but will require the least amount of RAM"> 109 <param name="coverage_dtype" type="select" label="Choose the dtype to use for storing coverage information" help="This affects the maximum recorded value for a position, e.g. uint8 would be 255 coverage, but will require the least amount of RAM">
110 <option value="guess" selected="True">Guess</option>
110 <option value="uint8">uint8</option> 111 <option value="uint8">uint8</option>
111 <option value="uint16">uint16</option> 112 <option value="uint16">uint16</option>
112 <option value="uint32">uint32</option> 113 <option value="uint32">uint32</option>
113 <option value="uint64" selected="True">uint64</option> 114 <option value="uint64">uint64</option>
114 </param> 115 </param>
115 <param name="safe" type="boolean" truevalue="--safe" falsevalue="" checked="False" label="Be extra safe"/> 116 <param name="safe" type="boolean" truevalue="--safe" falsevalue="" checked="False" label="Be extra safe"/>
116 </when> 117 </when>
117 </conditional> 118 </conditional>
118 119