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comparison bcftools_annotate.xml @ 17:8a2e296c07ef draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author iuc
date Tue, 20 Sep 2022 12:53:07 +0000
parents 2958e3b49ad4
children
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equal deleted inserted replaced
16:e075b1be5abb 17:8a2e296c07ef
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>Annotate and edit VCF/BCF files</description> 3 <description>Annotate and edit VCF/BCF files</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">annotate</token> 5 <token name="@EXECUTABLE@">annotate</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
63 --set-id '${section.set_id}' 63 --set-id '${section.set_id}'
64 #end if 64 #end if
65 #if $section.mark_sites: 65 #if $section.mark_sites:
66 --mark-sites '${section.mark_sites}' 66 --mark-sites '${section.mark_sites}'
67 #end if 67 #end if
68 #if $section.min_overlap
69 --min-overlap '$section.min_overlap'
70 #end if
68 71
69 #set $section = $sec_annotate 72 #set $section = $sec_annotate
70 #if $section.rename_chrs: 73 #if $section.rename_chrs:
71 --rename-chrs '${section.rename_chrs}' 74 --rename-chrs '${section.rename_chrs}'
72 #end if 75 #end if
73 #if $section.remove: 76 #if $section.remove:
74 --remove '${section.remove}' 77 --remove '${section.remove}'
75 #end if 78 #end if
79 #if $section.rename_annots
80 --rename-annots '$section.rename_annots'
81 #end if
82
76 83
77 ## Default section 84 ## Default section
78 #set $section = $sec_restrict 85 #set $section = $sec_restrict
79 @INCLUDE@ 86 @INCLUDE@
80 @EXCLUDE@ 87 @EXCLUDE@
128 </param> 135 </param>
129 </when> 136 </when>
130 </conditional> 137 </conditional>
131 <param argument="--mark-sites" type="text" value="" label="Mark Sites TAG" 138 <param argument="--mark-sites" type="text" value="" label="Mark Sites TAG"
132 help="add INFO/TAG flag to sites which are (&quot;+&quot;) or are not (&quot;-&quot;) listed in the annotations file" /> 139 help="add INFO/TAG flag to sites which are (&quot;+&quot;) or are not (&quot;-&quot;) listed in the annotations file" />
140 <param argument="--min-overlap" type="text" value="" label="Minimum required overlap of intersecting regions" optional="true" help="Minimum overlap required as a fraction of the variant in the annotation -a file (ANN), in the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF). By default overlaps of arbitrary length are sufficient.">
141 <sanitizer invalid_char="">
142 <valid initial="string.digits">
143 <add value=":" />
144 <add value="." />
145 </valid>
146 </sanitizer>
147 <validator type="regex">[0-9.:]+</validator>
148 </param>
133 <param argument="--set-id" type="text" value="" optional="true" label="Set Id"> 149 <param argument="--set-id" type="text" value="" optional="true" label="Set Id">
134 <help>Assign ID on the fly using the given format. 150 <help>Assign ID on the fly using the given format.
135 By default all existing IDs are replaced. 151 By default all existing IDs are replaced.
136 If the format string is preceded by "+", only missing IDs will be set. 152 If the format string is preceded by "+", only missing IDs will be set.
137 For example: '%CHROM\_%POS\_%REF\_%FIRST_ALT' 153 For example: '%CHROM\_%POS\_%REF\_%FIRST_ALT'
151 ]]></help> 167 ]]></help>
152 <validator type="regex" message="">^(\^?[A-Z]+(/\w+)?(,\^?[A-Z]+(/\w+)?)*)?$</validator> 168 <validator type="regex" message="">^(\^?[A-Z]+(/\w+)?(,\^?[A-Z]+(/\w+)?)*)?$</validator>
153 </param> 169 </param>
154 <param argument="--rename-chrs" type="data" format="tabular" label="Rename CHROM" optional="true" 170 <param argument="--rename-chrs" type="data" format="tabular" label="Rename CHROM" optional="true"
155 help="rename chromosomes according to the map in file, with old_name new_name pairs separated by whitespaces, each on a separate line." /> 171 help="rename chromosomes according to the map in file, with old_name new_name pairs separated by whitespaces, each on a separate line." />
172 <param argument="--rename-annots" type="data" format="tabular" optional="true" label="Rename annotations" help="TYPE/old\tnew, where TYPE is one of FILTER,INFO,FORMAT" />
156 </section> 173 </section>
157 <section name="sec_restrict" expanded="false" title="Restrict to"> 174 <section name="sec_restrict" expanded="false" title="Restrict to">
158 <expand macro="macro_include" /> 175 <expand macro="macro_include" />
159 <expand macro="macro_exclude" /> 176 <expand macro="macro_exclude" />
160 <expand macro="macro_collapse" /> 177 <expand macro="macro_collapse" />
272 <assert_contents> 289 <assert_contents>
273 <not_has_text text="GT:X:PL:Y:AA" /> 290 <not_has_text text="GT:X:PL:Y:AA" />
274 </assert_contents> 291 </assert_contents>
275 </output> 292 </output>
276 </test> 293 </test>
277 294 <!-- Test region overlap option -->
295 <test>
296 <param name="input_file" ftype="vcf" value="annotate3.vcf" />
297 <param name="anno_fmt" value="none" />
298 <param name="remove" value="FORMAT" />
299 <param name="output_type" value="v" />
300 <section name="sec_restrict">
301 <param name="regions_overlap" value="1"/>
302 </section>
303 <output name="output_file">
304 <assert_contents>
305 <not_has_text text="GT:X:PL:Y:AA" />
306 </assert_contents>
307 </output>
308 <assert_command>
309 <has_text text="--regions-overlap" />
310 </assert_command>
311 </test>
312 <!-- Test min overlap option -->
313 <test>
314 <param name="input_file" ftype="vcf" value="annotate3.vcf" />
315 <param name="anno_fmt" value="none" />
316 <param name="remove" value="FORMAT" />
317 <param name="output_type" value="v" />
318 <section name="sec_annofile">
319 <param name="min_overlap" value="0.5"/>
320 </section>
321 <output name="output_file">
322 <assert_contents>
323 <not_has_text text="GT:X:PL:Y:AA" />
324 </assert_contents>
325 </output>
326 <assert_command>
327 <has_text text="--min-overlap" />
328 </assert_command>
329 </test>
278 </tests> 330 </tests>
279 <help><![CDATA[ 331 <help><![CDATA[
280 ================================== 332 ==================================
281 bcftools @EXECUTABLE@ 333 bcftools @EXECUTABLE@
282 ================================== 334 ==================================