Mercurial > repos > iuc > bcftools_view

comparison bcftools_view.xml @ 13:98d5499ead46 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"
author iuc
date Tue, 13 Apr 2021 15:19:30 +0000
parents c4a9b38b435d
children 1d1762860d7e
comparison
equal deleted inserted replaced
12:23680a42e149 13:98d5499ead46
36 --min-ac ${section.min_ac} 36 --min-ac ${section.min_ac}
37 #end if 37 #end if
38 #if str($section.max_ac) 38 #if str($section.max_ac)
39 --max-ac ${section.max_ac} 39 --max-ac ${section.max_ac}
40 #end if 40 #end if
41 #if str($section.select_genotype) != "__none__": 41 #if str($section.select_genotype) != "None":
42 --genotype "${section.select_genotype}" 42 --genotype "${section.select_genotype}"
43 #end if 43 #end if
44 ## known or novel 44 ## known or novel
45 #if $section.known_or_novel: 45 #if $section.known_or_novel:
46 ${section.known_or_novel} 46 ${section.known_or_novel}
119 <section name="sec_filter" expanded="false" title="Filter Options"> 119 <section name="sec_filter" expanded="false" title="Filter Options">
120 <param name="min_ac" type="integer" label="Min Ac" optional="True" 120 <param name="min_ac" type="integer" label="Min Ac" optional="True"
121 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 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" />
122 <param name="max_ac" type="integer" label="Max Ac" optional="True" 122 <param name="max_ac" type="integer" label="Max Ac" optional="True"
123 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 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" />
124 <param name="select_genotype" type="select"> 124 <param name="select_genotype" type="select" label="Select Genotype" optional="True">
125 <option value="__none__" selected="True">No selection</option> 125 <help>
126 <option value="require one or more hom/het/missing genotype or" /> 126 Include only sites with one or more homozygous (hom), heterozygous (het) or missing (miss) genotypes.
127 <option value="if prefixed with &quot;^&quot;" /> 127 When prefixed with ^, the logic is reversed.
128 <option value="exclude sites with hom/het/missing genotypes" /> 128 Please notice that if the input file doesn't have any genotype columns,
129 then this option is ignored altogether.
130 </help>
131 <option value="hom">hom</option>
132 <option value="het">het</option>
133 <option value="miss">miss</option>
134 <option value="^hom">^hom</option>
135 <option value="^het">^het</option>
136 <option value="^miss">^miss</option>
129 </param> 137 </param>
130
131 <param name="types" type="select" label="Select Types" multiple="true" optional="True"> 138 <param name="types" type="select" label="Select Types" multiple="true" optional="True">
132 <help> 139 <help>
133 List of variant types to select. Site is selected if any of the ALT alleles is of the type requested. 140 List of variant types to select. Site is selected if any of the ALT alleles is of the type requested.
134 Types are determined by comparing the REF and ALT alleles in the VCF record. 141 Types are determined by comparing the REF and ALT alleles in the VCF record.
135 </help> 142 </help>
343 <not_has_text text="rs62584840" /> 350 <not_has_text text="rs62584840" />
344 <has_text text="2343543" /> 351 <has_text text="2343543" />
345 </assert_contents> 352 </assert_contents>
346 </output> 353 </output>
347 </test> 354 </test>
355 <test>
356 <param name="input_file" ftype="vcf" value="view.vcf" />
357 <param name="phased" value="--phased" />
358 <param name="output_type" value="v" />
359 <param name="select_genotype" value="^het" />
360 <output name="output_file">
361 <assert_contents>
362 <has_text text="--genotype ^het" />
363 <has_text text="rs78249411" />
364 <not_has_text text="3048719" />
365 </assert_contents>
366 </output>
367 </test>
348 </tests> 368 </tests>
349 <help><![CDATA[ 369 <help><![CDATA[
350 ===================================== 370 =====================================
351 bcftools @EXECUTABLE@ 371 bcftools @EXECUTABLE@
352 ===================================== 372 =====================================