Mercurial > repos > iuc > bcftools_norm

comparison bcftools_norm.xml @ 17:48291658fdf6 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 12:51:07 +0000
parents 481476814acc
children 271965b55437
comparison
equal deleted inserted replaced
16:021693fdadaa 17:48291658fdf6
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@"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows</description> 3 <description>Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">norm</token> 5 <token name="@EXECUTABLE@">norm</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
40 --check-ref $check_ref 40 --check-ref $check_ref
41 $normalize_indels 41 $normalize_indels
42 #if $rm_dup: 42 #if $rm_dup:
43 --rm-dup "$rm_dup" 43 --rm-dup "$rm_dup"
44 #end if 44 #end if
45 $atomize
46 #if $old_rec_tag
47 --old-rec-tag '$old_rec_tag'
48 #end if
45 #if $multiallelics.mode: 49 #if $multiallelics.mode:
46 --multiallelics '${multiallelics.mode}${multiallelics.multiallelic_types}' 50 --multiallelics '${multiallelics.mode}${multiallelics.multiallelic_types}'
47 #end if 51 #end if
48 #if $multiallelics.mode == '+': 52 #if $multiallelics.mode == '+':
49 ${multiallelics.strict_filter} 53 ${multiallelics.strict_filter}
50 #end if 54 #end if
55
51 #if $sec_default.site_win: 56 #if $sec_default.site_win:
52 --site-win ${sec_default.site_win} 57 --site-win ${sec_default.site_win}
53 #end if 58 #end if
54 59
55 #set $section = $sec_restrict 60 #set $section = $sec_restrict
76 <option value="w">ignore the problem (-w)</option> 81 <option value="w">ignore the problem (-w)</option>
77 <option value="wx">exclude the variant record from the output (-wx)</option> 82 <option value="wx">exclude the variant record from the output (-wx)</option>
78 <option value="ws">fix the variant record using the reference genome information (-ws)</option> 83 <option value="ws">fix the variant record using the reference genome information (-ws)</option>
79 <option value="e">exit with an error (-e)</option> 84 <option value="e">exit with an error (-e)</option>
80 </param> 85 </param>
86 <param argument="--atomize" type="boolean" truevalue="--atomize" falsevalue="" checked="false"
87 label="Atomize" help="Decompose complex variants (e.g. MNVs become consecutive SNVs)" />
81 <param argument="--do-not-normalize" name="normalize_indels" type="boolean" truevalue="" falsevalue="--do-not-normalize" checked="false" 88 <param argument="--do-not-normalize" name="normalize_indels" type="boolean" truevalue="" falsevalue="--do-not-normalize" checked="false"
82 label="Left-align and normalize indels?" /> 89 label="Left-align and normalize indels?" />
90 <param argument="--old-rec-tag" type="text" value="" optional="true" label="Annotate modified records with INFO/STR indicating the original variant">
91 <sanitizer invalid_char="">
92 <valid initial="string.letters,string.digits">
93 <add value="_" />
94 <add value="/" />
95 </valid>
96 </sanitizer>
97 <validator type="regex">[0-9a-zA-Z_/]+</validator>
98 </param>
83 <param name="rm_dup" type="select" display="radio" 99 <param name="rm_dup" type="select" display="radio"
84 label="Perform deduplication for the folowing types of variant records"> 100 label="Perform deduplication for the folowing types of variant records">
85 <option value="">do not deduplicate any records</option> 101 <option value="">do not deduplicate any records</option>
86 <option value="snps">snps</option> 102 <option value="snps">snps</option>
87 <option value="indels">indels</option> 103 <option value="indels">indels</option>
117 </when> 133 </when>
118 </conditional> 134 </conditional>
119 <section name="sec_restrict" expanded="false" title="Restrict all operations to"> 135 <section name="sec_restrict" expanded="false" title="Restrict all operations to">
120 <expand macro="macro_restrict" type="region" label_type="Region" /> 136 <expand macro="macro_restrict" type="region" label_type="Region" />
121 <expand macro="macro_restrict" type="target" label_type="Target"> 137 <expand macro="macro_restrict" type="target" label_type="Target">
122 <expand macro="macro_invert_targets" /> 138 <expand macro="macro_invert_targets" />
123 </expand> 139 </expand>
124 </section> 140 </section>
125 141
126 <section name="sec_default" expanded="false" title="Other Options"> 142 <section name="sec_default" expanded="false" title="Other Options">
127 <param name="site_win" type="integer" label="Site Window" value="1000" optional="True" 143 <param name="site_win" type="integer" label="Site Window" value="1000" optional="True"
232 <has_text_matching expression="2\t101\t.\tA\tc\t999\tPASS"/> 248 <has_text_matching expression="2\t101\t.\tA\tc\t999\tPASS"/>
233 <has_text_matching expression="2\t105\t.\tT\t&lt;DEL&gt;\t999\tPASS"/> 249 <has_text_matching expression="2\t105\t.\tT\t&lt;DEL&gt;\t999\tPASS"/>
234 </assert_contents> 250 </assert_contents>
235 </output> 251 </output>
236 </test> 252 </test>
237 253
254 <!-- Test atomize option -->
255 <test>
256 <param name="input_file" ftype="vcf" value="norm.split.vcf" />
257 <expand macro="test_using_reference" ref="norm.fa" />
258 <param name="normalize_indels" value="true" />
259 <conditional name="multiallelics">
260 <param name="mode" value="-" />
261 </conditional>
262 <param name="atomize" value="true"/>
263 <param name="output_type" value="v" />
264 <output name="output_file">
265 <assert_contents>
266 <not_has_text text="TAA,TAACCCTAAA" />
267 <has_text_matching expression="1\t105\t.\tTAAACCCTA\tT\t"/>
268 <has_text_matching expression="1\t105\t.\tTA\tT\t"/>
269 </assert_contents>
270 </output>
271 <assert_command>
272 <has_text text="--atomize" />
273 </assert_command>
274 </test>
275 <!-- Test region overlap options -->
276 <test>
277 <param name="input_file" ftype="vcf" dbkey="?" value="norm.vcf" />
278 <expand macro="test_using_reference" select_from="cached" ref="norm" />
279 <param name="normalize_indels" value="true" />
280 <param name="output_type" value="v" />
281 <section name="sec_restrict">
282 <param name="regions_overlap" value="1"/>
283 </section>
284 <output name="output_file">
285 <assert_contents>
286 <has_text text="T,TAACCCTA" />
287 <not_has_text text="TAA,TAACCCTAAA" />
288 </assert_contents>
289 </output>
290 <assert_command>
291 <has_text text="--regions-overlap" />
292 </assert_command>
293 </test>
238 </tests> 294 </tests>
239 <help><![CDATA[ 295 <help><![CDATA[
240 ===================================== 296 =====================================
241 bcftools @EXECUTABLE@ 297 bcftools @EXECUTABLE@
242 ===================================== 298 =====================================