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comparison tools/naive_variant_caller.xml @ 9:4fab5fce1adb

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Fix typo ("with with").
author Daniel Blankenberg <dan@bx.psu.edu>
date Tue, 31 Mar 2015 11:11:15 -0400
parents d5f866df45ae
children 8af4e7a4d041
comparison
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8:d5f866df45ae 9:4fab5fce1adb
91 <param name="min_support_depth" type="integer" value="0" min="0" label="Minimum number of reads needed to consider a REF/ALT" /> 91 <param name="min_support_depth" type="integer" value="0" min="0" label="Minimum number of reads needed to consider a REF/ALT" />
92 <param name="min_base_quality" type="integer" value="" label="Minimum base quality" optional="True" /> 92 <param name="min_base_quality" type="integer" value="" label="Minimum base quality" optional="True" />
93 <param name="min_mapping_quality" type="integer" value="" label="Minimum mapping quality" optional="True" /> 93 <param name="min_mapping_quality" type="integer" value="" label="Minimum mapping quality" optional="True" />
94 94
95 <param name="ploidy" type="integer" value="2" min="1" label="Ploidy" /> 95 <param name="ploidy" type="integer" value="2" min="1" label="Ploidy" />
96 <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 possible alternate alleles"/>
97 97
98 <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"/>
99 99
100 <conditional name="advanced_options"> 100 <conditional name="advanced_options">
101 <param name="advanced_options_selector" type="select" label="Show Advanced Options"> 101 <param name="advanced_options_selector" type="select" label="Show Advanced Options">
172 172
173 Ploidy: 173 Ploidy:
174 174
175 The number of genotype calls to make at each reported position. 175 The number of genotype calls to make at each reported position.
176 176
177 Only write out positions with with possible alternate alleles: 177 Only write out positions with possible alternate alleles:
178 178
179 When set, only positions which have at least one non-reference nucleotide which passes declare filters will be present in the output. 179 When set, only positions which have at least one non-reference nucleotide which passes declare filters will be present in the output.
180 180
181 Report counts by strand: 181 Report counts by strand:
182 182