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comparison intersectBed.xml @ 64:f6c88d2e9ae5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
author iuc
date Fri, 21 Feb 2025 21:38:34 +0000
parents 9f6bd4c9479f
children
comparison
equal deleted inserted replaced
63:7411007544bf 64:f6c88d2e9ae5
1 <tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> 1 <tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>find overlapping intervals in various ways</description> 2 <description>find overlapping intervals in various ways</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools" /> 6 <expand macro="bio_tools" />
7 <expand macro="requirements"> 7 <expand macro="requirements">
8 <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement> 8 <requirement type="package" version="1.18">samtools</requirement>
9 </expand> 9 </expand>
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <command><![CDATA[ 11 <command><![CDATA[
12 #import re 12 #import re
13 #set modes = ' '.join(str($overlap_mode).split(',')) 13 #set modes = ' '.join(str($overlap_mode).split(','))
91 <when value="default"/> 91 <when value="default"/>
92 <when value="specify"> 92 <when value="specify">
93 <expand macro="overlap" /> 93 <expand macro="overlap" />
94 <conditional name="reciprocal_cond"> 94 <conditional name="reciprocal_cond">
95 <expand macro="reciprocal" /> 95 <expand macro="reciprocal" />
96 <when value="-r"/> 96 <when value="-r"/>
97 <when value=""> 97 <when value="">
98 <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/> 98 <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
99 <param name="disjoint" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" 99 <param name="disjoint" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false"
100 label="Require that the fraction of overlap is fulfilled for A OR B." help="If enabled, then for -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered, otherwise, both fractions would have to be satisfied."/> 100 label="Require that the fraction of overlap is fulfilled for A OR B." help="If enabled, then for -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered, otherwise, both fractions would have to be satisfied."/>
101 </when> 101 </when>
102 </conditional> 102 </conditional>
103 </when> 103 </when>
104 </conditional> 104 </conditional>
105 <!-- -v --> 105 <!-- -v -->
106 <param name="invert" argument="-v" type="boolean" truevalue="-v" falsevalue="" checked="false" 106 <param name="invert" argument="-v" type="boolean" truevalue="-v" falsevalue="" checked="false"
107 label="Report only those alignments that **do not** overlap with file(s) B" /> 107 label="Report only those alignments that **do not** overlap with file(s) B" />
155 <param name="overlap_mode" value="-wa,-wb" /> 155 <param name="overlap_mode" value="-wa,-wb" />
156 <param name="sorted" value="true" /> 156 <param name="sorted" value="true" />
157 <output name="output" file="intersect-multiple-wa-wb.bed" ftype="bed" /> 157 <output name="output" file="intersect-multiple-wa-wb.bed" ftype="bed" />
158 </test> 158 </test>
159 <test> 159 <test>
160 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
161 <param name="inputA" value="intersect-query.bed" ftype="bed" /> 160 <param name="inputA" value="intersect-query.bed" ftype="bed" />
162 <conditional name="reduce_or_iterate"> 161 <conditional name="reduce_or_iterate">
163 <param name="reduce_or_iterate_selector" value="reduce" /> 162 <param name="reduce_or_iterate_selector" value="reduce" />
164 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" /> 163 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
165 <param name="names" value="yes" /> 164 <param name="names" value="yes" />
172 <param name="inputA" value="intersect-query.bed" ftype="bed" /> 171 <param name="inputA" value="intersect-query.bed" ftype="bed" />
173 <conditional name="reduce_or_iterate"> 172 <conditional name="reduce_or_iterate">
174 <param name="reduce_or_iterate_selector" value="reduce" /> 173 <param name="reduce_or_iterate_selector" value="reduce" />
175 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" /> 174 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
176 </conditional> 175 </conditional>
177 <param name="invert" value="-v" /> 176 <param name="invert" value="true" />
178 <param name="sorted" value="true" /> 177 <param name="sorted" value="true" />
179 <output name="output" file="intersect-multiple-invert.bed" ftype="bed" /> 178 <output name="output" file="intersect-multiple-invert.bed" ftype="bed" />
180 </test> 179 </test>
181 <test> 180 <test>
182 <param name="inputA" value="intersect-query.bed" ftype="bed" /> 181 <param name="inputA" value="intersect-query.bed" ftype="bed" />
250 <param name="inputA" value="intersect-A.bed" ftype="bed" /> 249 <param name="inputA" value="intersect-A.bed" ftype="bed" />
251 <conditional name="reduce_or_iterate"> 250 <conditional name="reduce_or_iterate">
252 <param name="reduce_or_iterate_selector" value="iterate" /> 251 <param name="reduce_or_iterate_selector" value="iterate" />
253 <param name="inputB" value="intersect-B.bed" ftype="bed" /> 252 <param name="inputB" value="intersect-B.bed" ftype="bed" />
254 </conditional> 253 </conditional>
255 <param name="once" value="-u" /> 254 <param name="once" value="true" />
256 <output name="output" file="intersect-unique.bed" ftype="bed" /> 255 <output name="output" file="intersect-unique.bed" ftype="bed" />
257 </test> 256 </test>
258 <test> 257 <test>
259 <param name="inputA" value="intersect-A.bed" ftype="bed" /> 258 <param name="inputA" value="intersect-A.bed" ftype="bed" />
260 <conditional name="reduce_or_iterate"> 259 <conditional name="reduce_or_iterate">
261 <param name="reduce_or_iterate_selector" value="iterate" /> 260 <param name="reduce_or_iterate_selector" value="iterate" />
262 <param name="inputB" value="intersect-B.bed" ftype="bed" /> 261 <param name="inputB" value="intersect-B.bed" ftype="bed" />
263 </conditional> 262 </conditional>
264 <param name="count" value="-c"/> 263 <param name="count" value="true"/>
265 <output name="output" file="intersect-count.bed" ftype="bed" /> 264 <output name="output" file="intersect-count.bed" ftype="bed" />
266 </test> 265 </test>
267 <test> 266 <test>
268 <param name="inputA" value="intersect-A.bed" ftype="bed" /> 267 <param name="inputA" value="intersect-A.bed" ftype="bed" />
269 <conditional name="reduce_or_iterate"> 268 <conditional name="reduce_or_iterate">
270 <param name="reduce_or_iterate_selector" value="iterate" /> 269 <param name="reduce_or_iterate_selector" value="iterate" />
271 <param name="inputB" value="intersect-B.bed" ftype="bed" /> 270 <param name="inputB" value="intersect-B.bed" ftype="bed" />
272 </conditional> 271 </conditional>
273 <param name="invert" value="-v"/> 272 <param name="invert" value="true"/>
274 <output name="output" file="intersect-invert.bed" ftype="bed" /> 273 <output name="output" file="intersect-invert.bed" ftype="bed" />
275 </test> 274 </test>
276 <test> 275 <test>
277 <param name="inputA" value="intersect-A2.bed" ftype="bed" /> 276 <param name="inputA" value="intersect-A2.bed" ftype="bed" />
278 <conditional name="reduce_or_iterate"> 277 <conditional name="reduce_or_iterate">
328 <conditional name="fraction_cond"> 327 <conditional name="fraction_cond">
329 <param name="fraction_select" value="specify"/> 328 <param name="fraction_select" value="specify"/>
330 <param name="overlap" value="0.5" /> 329 <param name="overlap" value="0.5" />
331 <conditional name="reciprocal_cond"> 330 <conditional name="reciprocal_cond">
332 <param name="overlapB" value="0.5" /> 331 <param name="overlapB" value="0.5" />
333 <param name="disjoint" value="-e" /> 332 <param name="disjoint" value="true" />
334 </conditional> 333 </conditional>
335 </conditional> 334 </conditional>
336 <output name="output" file="intersect-fracA.bed" ftype="bed" /> 335 <output name="output" file="intersect-fracA.bed" ftype="bed" />
337 </test> 336 </test>
338 <!-- old tests --> 337 <!-- old tests -->
339 <test> 338 <test>
340 <param name="inputA" value="intersectBed1.bed" ftype="bed" /> 339 <param name="inputA" value="intersectBed1.bed" ftype="bed" />
341 <param name="inputB" value="intersectBed2.bed" ftype="bed" /> 340 <conditional name="reduce_or_iterate">
341 <param name="inputB" value="intersectBed2.bed" ftype="bed" />
342 </conditional>
342 <param name="overlap_mode" value="-wa" /> 343 <param name="overlap_mode" value="-wa" />
343 <param name="split" value="False" /> 344 <param name="split" value="False" />
344 <output name="output" file="intersectBed_result1.bed" ftype="bed" /> 345 <output name="output" file="intersectBed_result1.bed" ftype="bed" />
345 </test> 346 </test>
346 <test> 347 <test>
347 <param name="inputA" value="intersectBed1.bed" ftype="bed" /> 348 <param name="inputA" value="intersectBed1.bed" ftype="bed" />
348 <param name="inputB" value="intersectBed2.bed" ftype="bed" /> 349 <conditional name="reduce_or_iterate">
350 <param name="inputB" value="intersectBed2.bed" ftype="bed" />
351 </conditional>
349 <param name="overlap_mode" value="-wa,-wb" /> 352 <param name="overlap_mode" value="-wa,-wb" />
350 <param name="split" value="False" /> 353 <param name="split" value="False" />
351 <output name="output" file="intersectBed_result2.bed" ftype="bed" /> 354 <output name="output" file="intersectBed_result2.bed" ftype="bed" />
352 </test> 355 </test>
353 <test> 356 <test>
354 <param name="inputA" value="intersectBed1.bed" ftype="bed" /> 357 <param name="inputA" value="intersectBed1.bed" ftype="bed" />
355 <param name="inputB" value="intersectBed2.bed" ftype="bed" /> 358 <conditional name="reduce_or_iterate">
359 <param name="inputB" value="intersectBed2.bed" ftype="bed" />
360 </conditional>
356 <param name="invert" value="True" /> 361 <param name="invert" value="True" />
357 <param name="split" value="False" /> 362 <param name="split" value="False" />
358 <output name="output" file="intersectBed_result3.bed" ftype="bed" /> 363 <output name="output" file="intersectBed_result3.bed" ftype="bed" />
359 </test> 364 </test>
360 </tests> 365 </tests>