Mercurial > repos > jjohnson > bcftools_annotate

comparison bcftools_annotate.xml @ 1:6c6a06ac35c1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sun, 26 Jun 2016 15:31:54 -0400
parents a30804010531
children
comparison
equal deleted inserted replaced
0:a30804010531 1:6c6a06ac35c1
133 Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter. 133 Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter.
134 Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT. 134 Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT.
135 To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER). 135 To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER).
136 "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT". 136 "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT".
137 ]]></help> 137 ]]></help>
138 <validator type="regex" message="">^([+]?(%[A-Z]+)(\_%[A-Z]+)*)?$</validator> 138 <validator type="regex" message="">^(\^?[A-Z]+(/\w+)?(,\^?[A-Z]+(/\w+)?)*)?$</validator>
139 </param> 139 </param>
140 <param name="rename_chrs" type="data" format="tabular" label="Rename CHROM" optional="True" 140 <param name="rename_chrs" type="data" format="tabular" label="Rename CHROM" optional="True"
141 help="rename chromosomes according to the map in file, with old_name new_name pairs separated by whitespaces, each on a separate line." /> 141 help="rename chromosomes according to the map in file, with old_name new_name pairs separated by whitespaces, each on a separate line." />
142 </section> 142 </section>
143 <section name="sec_restrict" expanded="false" title="Restrict to"> 143 <section name="sec_restrict" expanded="false" title="Restrict to">
223 <param name="anno_fmt" value="none" /> 223 <param name="anno_fmt" value="none" />
224 <param name="remove" value="ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL" /> 224 <param name="remove" value="ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL" />
225 <param name="output_type" value="v" /> 225 <param name="output_type" value="v" />
226 <output name="output_file"> 226 <output name="output_file">
227 <assert_contents> 227 <assert_contents>
228 <not_has_text text="ID=X" /> 228 <not_has_text text="fltY" />
229 </assert_contents> 229 </assert_contents>
230 </output> 230 </output>
231 </test> 231 </test>
232 <test> 232 <test>
233 <param name="input_file" ftype="vcf" value="annotate3.vcf" /> 233 <param name="input_file" ftype="vcf" value="annotate3.vcf" />
234 <param name="anno_fmt" value="none" /> 234 <param name="anno_fmt" value="none" />
235 <param name="remove" value="FORMAT" /> 235 <param name="remove" value="FORMAT" />
236 <param name="output_type" value="v" /> 236 <param name="output_type" value="v" />
237 <output name="output_file"> 237 <output name="output_file">
238 <assert_contents> 238 <assert_contents>
239 <not_has_text text="ID=PL" /> 239 <not_has_text text="GT:X:PL:Y:AA" />
240 </assert_contents> 240 </assert_contents>
241 </output> 241 </output>
242 </test> 242 </test>
243 243
244 </tests> 244 </tests>