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comparison bcftools_view.xml @ 2:cc016cb332cd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 44bebb8a97d64015cbba59f0663e2541035112b6
author iuc
date Mon, 03 Oct 2016 12:21:48 -0400
parents 94f98eb08abc
children 993ed534cc38
comparison
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1:3e4c1bb306e9 2:cc016cb332cd
114 help="Do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)" /> 114 help="Do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)" />
115 <param name="trim_alt_alleles" type="boolean" truevalue="--trim-alt-alleles" falsevalue="" label="Trim Alt Alleles" 115 <param name="trim_alt_alleles" type="boolean" truevalue="--trim-alt-alleles" falsevalue="" label="Trim Alt Alleles"
116 help="Trim alternate alleles not seen in the subset" /> 116 help="Trim alternate alleles not seen in the subset" />
117 </section> 117 </section>
118 <section name="sec_filter" expanded="false" title="Filter Options"> 118 <section name="sec_filter" expanded="false" title="Filter Options">
119 <param name="min_ac" type="integer" label="Min Ac" default="nref" optional="True" 119 <param name="min_ac" type="integer" label="Min Ac" optional="True"
120 help="(-c --min-ac) Minimum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" /> 120 help="(-c --min-ac) Minimum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
121 <param name="max_ac" type="integer" label="Max Ac" default="nref" optional="True" 121 <param name="max_ac" type="integer" label="Max Ac" optional="True"
122 help="(-C --max-ac) Maximum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" /> 122 help="(-C --max-ac) Maximum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
123 <param name="select_genotype" type="select"> 123 <param name="select_genotype" type="select">
124 <option value="__none__" selected="True">No selection</option> 124 <option value="__none__" selected="True">No selection</option>
125 <option value="require one or more hom/het/missing genotype or" /> 125 <option value="require one or more hom/het/missing genotype or" />
126 <option value="if prefixed with &quot;^&quot;" /> 126 <option value="if prefixed with &quot;^&quot;" />
161 <option value="--phased">(-p) print sites where all samples are phased</option> 161 <option value="--phased">(-p) print sites where all samples are phased</option>
162 <option value="--exclude-phased">(-P) exclude sites where all samples are phased</option> 162 <option value="--exclude-phased">(-P) exclude sites where all samples are phased</option>
163 </param> 163 </param>
164 164
165 <!-- TODO optional select for type: nref,alt1,minor,major,sum --> 165 <!-- TODO optional select for type: nref,alt1,minor,major,sum -->
166 <param name="min_af" type="float" label="Min Af" default="nref" optional="True" 166 <param name="min_af" type="float" label="Min Af" optional="True"
167 help="(-q) Minimum frequency for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" /> 167 help="(-q) Minimum frequency for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
168 <param name="max_af" type="float" label="Max Af" default="nref" optional="True" 168 <param name="max_af" type="float" label="Max Af" optional="True"
169 help="(-Q) Maximum frequency for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" /> 169 help="(-Q) Maximum frequency for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
170 170
171 <param name="uncalled" type="select" label="filter on genotype uncalled" optional="true"> 171 <param name="uncalled" type="select" label="filter on genotype uncalled" optional="true">
172 <option value="--uncalled">uncalled - print sites without a called genotype</option> 172 <option value="--uncalled">uncalled - print sites without a called genotype</option>
173 <option value="--exclude-uncalled">exclude-uncalled - exclude sites without a called genotype</option> 173 <option value="--exclude-uncalled">exclude-uncalled - exclude sites without a called genotype</option>
189 help="Drop individual genotype information (after subsetting if -s option set)" /> 189 help="Drop individual genotype information (after subsetting if -s option set)" />
190 <param name="header" type="select" label="output header" optional="true"> 190 <param name="header" type="select" label="output header" optional="true">
191 <option value="--no-header">(-h) no-header</option> 191 <option value="--no-header">(-h) no-header</option>
192 <option value="--header-only">(-H) header-only</option> 192 <option value="--header-only">(-H) header-only</option>
193 </param> 193 </param>
194 <param name="compression_level" type="integer" min="0" max="9" label="Compression Level" default="-1" optional="True" 194 <param name="compression_level" type="integer" min="0" max="9" label="Compression Level" optional="True"
195 help="Compression level: 0 uncompressed, 1 best speed, 9 best compression" /> 195 help="Compression level: 0 uncompressed, 1 best speed, 9 best compression" />
196 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets File" 196 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets File"
197 help="Inverts the query/filtering applied by Targets File" /> 197 help="Inverts the query/filtering applied by Targets File" />
198 </section> 198 </section>
199 <expand macro="macro_select_output_type" /> 199 <expand macro="macro_select_output_type" />