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comparison bcftools_view.xml @ 4:993ed534cc38 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
author iuc
date Sat, 11 Mar 2017 18:05:59 -0500
parents cc016cb332cd
children 741a08398a04
comparison
equal deleted inserted replaced
3:cde34352778e 4:993ed534cc38
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="@VERSION@.0"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@">
3 <description>VCF/BCF conversion, view, subset and filter VCF/BCF files</description> 3 <description>VCF/BCF conversion, view, subset and filter VCF/BCF files</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">view</token> 5 <token name="@EXECUTABLE@">view</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 <xml name="macro_types_options"> 7 <xml name="macro_types_options">
29 ${section.force_samples} 29 ${section.force_samples}
30 30
31 31
32 ## Filter section 32 ## Filter section
33 #set $section = $sec_filter 33 #set $section = $sec_filter
34 #if $section.min_ac: 34 #if str($section.min_ac)
35 --min-ac "${section.min_ac}" 35 --min-ac ${section.min_ac}
36 #end if 36 #end if
37 #if $section.max_ac: 37 #if str($section.max_ac)
38 --max-ac "${section.max_ac}" 38 --max-ac ${section.max_ac}
39 #end if 39 #end if
40 #if str($section.select_genotype) != "__none__": 40 #if str($section.select_genotype) != "__none__":
41 --genotype "${section.select_genotype}" 41 --genotype "${section.select_genotype}"
42 #end if 42 #end if
43 ## known or novel 43 ## known or novel
44 #if $section.known_or_novel: 44 #if $section.known_or_novel:
45 ${section.known_or_novel} 45 ${section.known_or_novel}
46 #end if 46 #end if
47 #if $section.min_alleles: 47 #if str($section.min_alleles)
48 --min-alleles "${section.min_alleles}" 48 --min-alleles ${section.min_alleles}
49 #end if 49 #end if
50 #if $section.max_alleles: 50 #if str($section.max_alleles)
51 --max-alleles "${section.max_alleles}" 51 --max-alleles ${section.max_alleles}
52 #end if 52 #end if
53 #if $section.phased: 53 #if $section.phased:
54 ${section.phased} 54 ${section.phased}
55 #end if 55 #end if
56 #if $section.min_af: 56 #if str($section.min_af)
57 --min-af "${section.min_af}" 57 --min-af ${section.min_af}
58 #end if 58 #end if
59 #if $section.max_af: 59 #if str($section.max_af)
60 --max-af "${section.max_af}" 60 --max-af ${section.max_af}
61 #end if 61 #end if
62 #if $section.uncalled: 62 #if $section.uncalled:
63 ${section.uncalled} 63 ${section.uncalled}
64 #end if 64 #end if
65 #if $section.types: 65 #if $section.types:
66 --types "${section.types}" 66 --types "${section.types}"
67 #end if 67 #end if
68 #if $section.exclude_types: 68 #if $section.exclude_types:
69 --exclude-types "${section.exclude_types}" 69 --exclude-types "${section.exclude_types}"
70 #end if 70 #end if
71 #if $section.private: 71 #if $section.private:
72 ${section.private} 72 ${section.private}
73 #end if 73 #end if
74 74
75 ## Output section 75 ## Output section
76 #set $section = $sec_output 76 #set $section = $sec_output
77 ${section.drop_genotypes} 77 ${section.drop_genotypes}
78 #if $section.header: 78 #if $section.header:
79 ${section.header} 79 ${section.header}
80 #end if 80 #end if
81 #if $section.compression_level: 81 #if str($section.compression_level)
82 --compression-level "${section.compression_level}" 82 --compression-level ${section.compression_level}
83 #end if 83 #end if
84 84
85 #set $section = $sec_restrict 85 #set $section = $sec_restrict
86 @APPLY_FILTERS@ 86 @APPLY_FILTERS@
87 @INCLUDE@ 87 @INCLUDE@
92 @OUTPUT_TYPE@ 92 @OUTPUT_TYPE@
93 @THREADS@ 93 @THREADS@
94 94
95 ## Primary Input/Outputs 95 ## Primary Input/Outputs
96 @INPUT_FILE@ 96 @INPUT_FILE@
97 > "$output_file" 97 > '$output_file'
98 ]]> 98 ]]>
99 </command> 99 </command>
100 <inputs> 100 <inputs>
101 <expand macro="macro_input" /> 101 <expand macro="macro_input" />
102 <section name="sec_restrict" expanded="false" title="Restrict to"> 102 <section name="sec_restrict" expanded="false" title="Restrict to">
106 <expand macro="macro_include" /> 106 <expand macro="macro_include" />
107 <expand macro="macro_exclude" /> 107 <expand macro="macro_exclude" />
108 </section> 108 </section>
109 <section name="sec_subset" expanded="false" title="Subset Options"> 109 <section name="sec_subset" expanded="false" title="Subset Options">
110 <expand macro="macro_samples" /> 110 <expand macro="macro_samples" />
111 <param name="force_samples" type="boolean" truevalue="--force-samples" falsevalue="" label="Force Samples" 111 <param name="force_samples" type="boolean" truevalue="--force-samples" falsevalue="" label="Force Samples"
112 help="Only warn about unknown subset samples" /> 112 help="Only warn about unknown subset samples" />
113 <param name="no_update" type="boolean" truevalue="--no-update" falsevalue="" label="No Update" 113 <param name="no_update" type="boolean" truevalue="--no-update" falsevalue="" label="No Update"
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" 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" 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;" />
127 <option value="exclude sites with hom/het/missing genotypes" /> 127 <option value="exclude sites with hom/het/missing genotypes" />
128 </param> 128 </param>
129 129
130 <param name="types" type="select" label="Select Types" multiple="true" optional="True"> 130 <param name="types" type="select" label="Select Types" multiple="true" optional="True">
131 <help> 131 <help>
132 List of variant types to select. Site is selected if any of the ALT alleles is of the type requested. 132 List of variant types to select. Site is selected if any of the ALT alleles is of the type requested.
133 Types are determined by comparing the REF and ALT alleles in the VCF record. 133 Types are determined by comparing the REF and ALT alleles in the VCF record.
134 </help> 134 </help>
135 <expand macro="macro_types_options" /> 135 <expand macro="macro_types_options" />
136 </param> 136 </param>
137 137
138 <param name="exclude_types" type="select" label="Exclude Types" multiple="true" optional="True"> 138 <param name="exclude_types" type="select" label="Exclude Types" multiple="true" optional="True">
139 <help> 139 <help>
140 List of variant types to exclude. Site is excluded if any of the ALT alleles is of the type requested. 140 List of variant types to exclude. Site is excluded if any of the ALT alleles is of the type requested.
141 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.
142 </help> 142 </help>
143 <expand macro="macro_types_options" /> 143 <expand macro="macro_types_options" />
144 </param> 144 </param>
145 145
147 <param name="known_or_novel" type="select" label="filter known or novel ID" optional="true"> 147 <param name="known_or_novel" type="select" label="filter known or novel ID" optional="true">
148 <option value="--novel">(-k) print novel sites only (ID column is ".")</option> 148 <option value="--novel">(-k) print novel sites only (ID column is ".")</option>
149 <option value="--known">(-n) print known sites only (ID column is not ".")</option> 149 <option value="--known">(-n) print known sites only (ID column is not ".")</option>
150 </param> 150 </param>
151 151
152 <param name="min_alleles" type="integer" label="Min Alleles" optional="True" 152 <param name="min_alleles" type="integer" label="Min Alleles" optional="True"
153 help="(-m) Minimum number of alleles listed in REF and ALT (e.g. -m2)" /> 153 help="(-m) Minimum number of alleles listed in REF and ALT (e.g. -m2)" />
154 <param name="max_alleles" type="integer" label="Max Alleles" optional="True" 154 <param name="max_alleles" type="integer" label="Max Alleles" optional="True"
155 help="(-M) Maximum number of alleles listed in REF and ALT (e.g. -M2 for biallelic sites)" /> 155 help="(-M) Maximum number of alleles listed in REF and ALT (e.g. -M2 for biallelic sites)" />
156 156
157 <param name="phased" type="select" label="filter phased" optional="true"> 157 <param name="phased" type="select" label="filter phased" optional="true">
158 <help> 158 <help>
159 Haploid genotypes are considered phased. Missing genotypes considered unphased unless the phased bit is set. 159 Haploid genotypes are considered phased. Missing genotypes considered unphased unless the phased bit is set.
160 </help> 160 </help>
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" 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" 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>
183 </param> 183 </param>
184 184
185 </section> 185 </section>
186 186
187 <section name="sec_output" expanded="false" title="Output Options"> 187 <section name="sec_output" expanded="false" title="Output Options">
188 <param name="drop_genotypes" type="boolean" truevalue="--drop-genotypes" falsevalue="" label="Drop Genotypes" 188 <param name="drop_genotypes" type="boolean" truevalue="--drop-genotypes" falsevalue="" label="Drop Genotypes"
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" 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" />
200 </inputs> 200 </inputs>
201 <outputs> 201 <outputs>
209 <param name="samples" value="NA00002" /> 209 <param name="samples" value="NA00002" />
210 <param name="types" value="snps" /> 210 <param name="types" value="snps" />
211 <param name="output_type" value="v" /> 211 <param name="output_type" value="v" />
212 <output name="output_file"> 212 <output name="output_file">
213 <assert_contents> 213 <assert_contents>
214 <has_text text="rs2298108" /> 214 <has_text text="rs2298108" />
215 <not_has_text text="rs6111385" /> 215 <not_has_text text="rs6111385" />
216 </assert_contents> 216 </assert_contents>
217 </output> 217 </output>
218 </test> 218 </test>
219 <test> 219 <test>
220 <param name="input_file" ftype="vcf" value="view.vcf" /> 220 <param name="input_file" ftype="vcf" value="view.vcf" />
223 <param name="samples" value="NA00003" /> 223 <param name="samples" value="NA00003" />
224 <param name="regions" value="20,Y" /> 224 <param name="regions" value="20,Y" />
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 <has_text text="8657215" /> 228 <has_text text="8657215" />
229 <not_has_text text="rs6111385" /> 229 <not_has_text text="rs6111385" />
230 </assert_contents> 230 </assert_contents>
231 </output> 231 </output>
232 </test> 232 </test>
233 <test> 233 <test>
234 <param name="input_file" ftype="vcf" value="view.vcf" /> 234 <param name="input_file" ftype="vcf" value="view.vcf" />
238 <param name="samples" value="NA00003" /> 238 <param name="samples" value="NA00003" />
239 <param name="regions" value="20,Y" /> 239 <param name="regions" value="20,Y" />
240 <param name="output_type" value="v" /> 240 <param name="output_type" value="v" />
241 <output name="output_file"> 241 <output name="output_file">
242 <assert_contents> 242 <assert_contents>
243 <has_text text="rs6111385" /> 243 <has_text text="rs6111385" />
244 <not_has_text text="8657215" /> 244 <not_has_text text="8657215" />
245 </assert_contents> 245 </assert_contents>
246 </output> 246 </output>
247 </test> 247 </test>
248 <test> 248 <test>
249 <param name="input_file" ftype="vcf" value="view.vcf" /> 249 <param name="input_file" ftype="vcf" value="view.vcf" />
250 <param name="private" value="--private" /> 250 <param name="private" value="--private" />
251 <param name="samples" value="NA00003" /> 251 <param name="samples" value="NA00003" />
252 <param name="output_type" value="v" /> 252 <param name="output_type" value="v" />
253 <output name="output_file"> 253 <output name="output_file">
254 <assert_contents> 254 <assert_contents>
255 <has_text text="rs62584840" /> 255 <has_text text="rs62584840" />
256 <not_has_text text="8657215" /> 256 <not_has_text text="8657215" />
257 </assert_contents> 257 </assert_contents>
258 </output> 258 </output>
259 </test> 259 </test>
260 <test> 260 <test>
261 <param name="input_file" ftype="vcf" value="view.vcf" /> 261 <param name="input_file" ftype="vcf" value="view.vcf" />
262 <param name="include" value="QUAL==999 &amp;&amp; (FS&lt;20 || FS&gt;=41.02) &amp;&amp; ICF&gt;-0.1 &amp;&amp; HWE*2&gt;1.2" /> 262 <param name="include" value="QUAL==999 &amp;&amp; (FS&lt;20 || FS&gt;=41.02) &amp;&amp; ICF&gt;-0.1 &amp;&amp; HWE*2&gt;1.2" />
263 <param name="output_type" value="v" /> 263 <param name="output_type" value="v" />
264 <output name="output_file"> 264 <output name="output_file">
265 <assert_contents> 265 <assert_contents>
266 <has_text text="rs5939407" /> 266 <has_text text="rs5939407" />
267 <not_has_text text="8657215" /> 267 <not_has_text text="8657215" />
268 </assert_contents> 268 </assert_contents>
269 </output> 269 </output>
270 </test> 270 </test>
271 <test> 271 <test>
272 <param name="input_file" ftype="vcf" value="view.vcf" /> 272 <param name="input_file" ftype="vcf" value="view.vcf" />
273 <param name="phased" value="--phased" /> 273 <param name="phased" value="--phased" />
274 <param name="output_type" value="v" /> 274 <param name="output_type" value="v" />
275 <output name="output_file"> 275 <output name="output_file">
276 <assert_contents> 276 <assert_contents>
277 <has_text text="rs78249411" /> 277 <has_text text="rs78249411" />
278 <not_has_text text="rs6111385" /> 278 <not_has_text text="rs6111385" />
279 </assert_contents> 279 </assert_contents>
280 </output> 280 </output>
281 </test> 281 </test>
282 <test> 282 <test>
283 <param name="input_file" ftype="vcf" value="view.vcf" /> 283 <param name="input_file" ftype="vcf" value="view.vcf" />
284 <param name="phased" value="--exclude-phased" /> 284 <param name="phased" value="--exclude-phased" />
285 <param name="output_type" value="v" /> 285 <param name="output_type" value="v" />
286 <output name="output_file"> 286 <output name="output_file">
287 <assert_contents> 287 <assert_contents>
288 <has_text text="rs6111385" /> 288 <has_text text="rs6111385" />
289 <not_has_text text="rs78249411" /> 289 <not_has_text text="rs78249411" />
290 </assert_contents> 290 </assert_contents>
291 </output> 291 </output>
292 </test> 292 </test>
293 <test> 293 <test>
294 <param name="input_file" ftype="vcf" value="view.vcf" /> 294 <param name="input_file" ftype="vcf" value="view.vcf" />
298 <param name="max_af" value="0.7" /> 298 <param name="max_af" value="0.7" />
299 <param name="header" value="--header-only" /> 299 <param name="header" value="--header-only" />
300 <param name="output_type" value="v" /> 300 <param name="output_type" value="v" />
301 <output name="output_file"> 301 <output name="output_file">
302 <assert_contents> 302 <assert_contents>
303 <has_text text="##bcftools_viewCommand" /> 303 <has_text text="##bcftools_viewCommand" />
304 <not_has_text text="rs78249411" /> 304 <not_has_text text="rs78249411" />
305 </assert_contents> 305 </assert_contents>
306 </output> 306 </output>
307 </test> 307 </test>
308 <test> 308 <test>
309 <param name="input_file" ftype="vcf" value="view.vcf" /> 309 <param name="input_file" ftype="vcf" value="view.vcf" />
310 <param name="uncalled" value="--uncalled" /> 310 <param name="uncalled" value="--uncalled" />
311 <param name="header" value="--no-header" /> 311 <param name="header" value="--no-header" />
312 <param name="output_type" value="v" /> 312 <param name="output_type" value="v" />
313 <output name="output_file"> 313 <output name="output_file">
314 <assert_contents> 314 <assert_contents>
315 <not_has_text text="##bcftools_viewCommand" /> 315 <not_has_text text="##bcftools_viewCommand" />
316 <has_text text="5464562" /> 316 <has_text text="5464562" />
317 </assert_contents> 317 </assert_contents>
318 </output> 318 </output>
319 </test> 319 </test>
320 <test> 320 <test>
321 <param name="input_file" ftype="vcf" value="view.vcf" /> 321 <param name="input_file" ftype="vcf" value="view.vcf" />
322 <param name="exclude_types" value="snps" /> 322 <param name="exclude_types" value="snps" />
323 <param name="drop_genotypes" value="true" /> 323 <param name="drop_genotypes" value="true" />
324 <param name="output_type" value="v" /> 324 <param name="output_type" value="v" />
325 <output name="output_file"> 325 <output name="output_file">
326 <assert_contents> 326 <assert_contents>
327 <not_has_text text="##FORMAT=&lt;ID=GT" /> 327 <not_has_text text="##FORMAT=&lt;ID=GT" />
328 <not_has_text text="rs62584840" /> 328 <not_has_text text="rs62584840" />
329 <has_text text="2343543" /> 329 <has_text text="2343543" />
330 </assert_contents> 330 </assert_contents>
331 </output> 331 </output>
332 </test> 332 </test>
333 </tests> 333 </tests>
334 <help><![CDATA[ 334 <help><![CDATA[