Mercurial > repos > blankenberg > naive_variant_caller

comparison tools/naive_variant_caller.xml @ 5:8398666758e3

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Update options.
author Daniel Blankenberg <dan@bx.psu.edu>
date Tue, 04 Feb 2014 17:26:26 -0500
parents ae6edc0012ba
children d5f866df45ae
comparison
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4:13d534f2bcde 5:8398666758e3
41 41
42 #if str($min_mapping_quality): 42 #if str($min_mapping_quality):
43 --min_mapping_quality "${min_mapping_quality}" 43 --min_mapping_quality "${min_mapping_quality}"
44 #end if 44 #end if
45 45
46 --coverage_dtype "${coverage_dtype}"
47
48 --allow_out_of_bounds_positions 46 --allow_out_of_bounds_positions
49 47
48 #if str( $advanced_options.advanced_options_selector ) == "advanced":
49 --coverage_dtype "${advanced_options.coverage_dtype}"
50 ${advanced_options.safe}
51 #else
52 --coverage_dtype "uint64"
53 #end if
50 </command> 54 </command>
51 <inputs> 55 <inputs>
52 <conditional name="reference_source"> 56 <conditional name="reference_source">
53 <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">
54 <option value="cached">Locally cached</option> 58 <option value="cached">Locally cached</option>
91 <param name="ploidy" type="integer" value="2" min="1" label="Ploidy" /> 95 <param name="ploidy" type="integer" value="2" min="1" label="Ploidy" />
92 <param name="variants_only" type="boolean" truevalue="--variants_only" falsevalue="" checked="False" label="Only write out positions with with possible alternate alleles"/> 96 <param name="variants_only" type="boolean" truevalue="--variants_only" falsevalue="" checked="False" label="Only write out positions with with possible alternate alleles"/>
93 97
94 <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="False" label="Report counts by strand"/> 98 <param name="use_strand" type="boolean" truevalue="--use_strand" falsevalue="" checked="False" label="Report counts by strand"/>
95 99
96 <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"> 100 <conditional name="advanced_options">
97 <option value="uint8">uint8</option> 101 <param name="advanced_options_selector" type="select" label="Show Advanced Options">
98 <option value="uint16" selected="True">uint16</option> 102 <option value="basic" selected="True">Hide Advanced Options</option>
99 <option value="uint32">uint32</option> 103 <option value="advanced">Show Advanced Options</option>
100 <option value="uint64">uint64</option> 104 </param>
101 </param> 105 <when value="basic">
106 <!-- Do nothing here -->
107 </when>
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">
110 <option value="uint8">uint8</option>
111 <option value="uint16">uint16</option>
112 <option value="uint32">uint32</option>
113 <option value="uint64" selected="True">uint64</option>
114 </param>
115 <param name="safe" type="boolean" truevalue="--safe" falsevalue="" checked="False" label="Be extra safe"/>
116 </when>
117 </conditional>
102 118
103 </inputs> 119 </inputs>
104 <outputs> 120 <outputs>
105 <data format="vcf" name="output_vcf" /> 121 <data format="vcf" name="output_vcf" />
106 </outputs> 122 </outputs>
198 <param name="min_base_quality" value="" /> 214 <param name="min_base_quality" value="" />
199 <param name="min_mapping_quality" value="" /> 215 <param name="min_mapping_quality" value="" />
200 <param name="ploidy" value="2" /> 216 <param name="ploidy" value="2" />
201 <param name="variants_only" value="False" /> 217 <param name="variants_only" value="False" />
202 <param name="use_strand" value="False" /> 218 <param name="use_strand" value="False" />
219 <param name="advanced_options_selector" value="advanced" />
203 <param name="coverage_dtype" value="uint8" /> 220 <param name="coverage_dtype" value="uint8" />
204 <output name="output_vcf" file="fake_phiX174_reads_1_test_out_1.vcf" compare="contains" /> 221 <output name="output_vcf" file="fake_phiX174_reads_1_test_out_1.vcf" compare="contains" />
205 </test> 222 </test>
206 </tests> 223 </tests>
207 224