annotate intersectBed.xml @ 46:64e2edfe7a2c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
author iuc
date Sat, 18 May 2024 23:28:38 +0000
parents 07e8b80f278c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
46
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 43
diff changeset
1 <tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
4
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 1
diff changeset
2 <description>find overlapping intervals in various ways</description>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
3 <macros>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
4 <import>macros.xml</import>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
5 </macros>
41
7ab85ac5f64b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
iuc
parents: 39
diff changeset
6 <expand macro="bio_tools" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
7 <expand macro="requirements">
46
64e2edfe7a2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4
iuc
parents: 43
diff changeset
8 <requirement type="package" version="1.18">samtools</requirement>
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
9 </expand>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
10 <expand macro="stdio" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
11 <command><![CDATA[
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
12 #import re
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
13 #set modes = ' '.join(str($overlap_mode).split(','))
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
14
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
15 #if $modes == "None":
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
16 #set modes = ''
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
17 #end if
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
18
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
19 bedtools intersect
37
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 35
diff changeset
20 -a '${inputA}'
28
6283d16e40ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 393e1fef41cfb7e28005a98fd5043a3f42347686
iuc
parents: 26
diff changeset
21
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
22 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
23 -b '$reduce_or_iterate.inputB'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
24 #else:
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
25 -b
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
26 #for $file in $reduce_or_iterate.inputB
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
27 '$file'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
28 #end for
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
29
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
30 #if $reduce_or_iterate.names:
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
31 #set namesB = "' '".join([re.sub('[^\s\w\-]', '_', str($file.element_identifier)) for $file in $reduce_or_iterate.inputB])
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
32 -names '$namesB'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
33 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
34 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
35 $split
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
36 $strand
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
37 #if $fraction_cond.fraction_select == "specify":
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
38 #if str($fraction_cond.overlap)
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
39 -f $fraction_cond.overlap
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
40 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
41 $fraction_cond.reciprocal_cond.reciprocal
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
42 #if str($fraction_cond.reciprocal_cond.reciprocal) == '':
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
43 #if str($fraction_cond.reciprocal_cond.overlapB):
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
44 -F $fraction_cond.reciprocal_cond.overlapB
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
45 #end if
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
46 $fraction_cond.reciprocal_cond.disjoint
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
47 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
48 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
49 $invert
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
50 $once
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
51 $header
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
52 $modes
37
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 35
diff changeset
53 @SORTED@
43
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents: 41
diff changeset
54 @GENOME_FILE@
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
55 $bed
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
56 $count
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
57 > '${output}'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
58 ]]></command>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
59 <inputs>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
60 <param name="inputA" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File A to intersect with B" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format" />
20
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a
iuc
parents: 13
diff changeset
61 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
62 <param name="reduce_or_iterate_selector" type="select" label="Combined or separate output files">
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
63 <option value="iterate" selected="true">One output file per 'input B' file</option>
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
64 <option value="reduce">Single output containing intersections of any 'input B' lines with A</option>
20
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a
iuc
parents: 13
diff changeset
65 </param>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
66 <when value="iterate">
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
67 <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@"
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
68 label="File B to intersect with A" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
20
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a
iuc
parents: 13
diff changeset
69 </when>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
70 <when value="reduce">
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
71 <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" multiple="true"
26
95a3b2c25bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
parents: 20
diff changeset
72 label="File(s) B to intersect with A" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
73 <param argument="-names" type="boolean" truevalue="yes" falsevalue="no" label="Add data set names instead of indices" />
20
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a
iuc
parents: 13
diff changeset
74 </when>
df56e1b12d0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 9f7b029951fa0f854c9c6a5f241ce9a20ae4f22a
iuc
parents: 13
diff changeset
75 </conditional>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
76 <expand macro="strand2" />
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
77 <param name="overlap_mode" type="select" multiple="true" label="What should be written to the output file?">
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
78 <option value="-wa">Write the original entry in A for each overlap (-wa)</option>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
79 <option value="-wb">Write the original entry in B for each overlap. Useful for knowing what A overlaps. Restricted by the fraction- and reciprocal option (-wb)</option>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
80 <option value="-wo">Write the original A and B entries plus the number of base pairs of overlap between the two features. Only A features with overlap are reported. Restricted by the fraction- and reciprocal option (-wo)</option>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
81 <option value="-wao">Write the original A and B entries plus the number of base pairs of overlap between the two features. However, A features w/o overlap are also reported with a NULL B feature and overlap = 0. Restricted by the fraction- and reciprocal option (-wao)</option>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
82 <option value="-loj">Perform a "left outer join". That is, for each feature in A report each overlap with B. If no overlaps are found, report a NULL feature for B (-loj)</option>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
83 </param>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
84
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
85 <expand macro="split" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
86 <conditional name="fraction_cond">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
87 <param name="fraction_select" type="select" label="Required overlap">
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
88 <option value="default" selected="true">Default: 1bp</option>
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
89 <option value="specify">Specify minimum overlap(s)</option>
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
90 </param>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
91 <when value="default"/>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
92 <when value="specify">
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
93 <expand macro="overlap" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
94 <conditional name="reciprocal_cond">
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
95 <expand macro="reciprocal" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
96 <when value="-r"/>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
97 <when value="">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
98 <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
99 <param name="disjoint" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false"
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
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."/>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
101 </when>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
102 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
103 </when>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
104 </conditional>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
105 <!-- -v -->
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
106 <param name="invert" argument="-v" type="boolean" truevalue="-v" falsevalue="" checked="false"
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
107 label="Report only those alignments that **do not** overlap with file(s) B" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
108 <!-- -u -->
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
109 <param name="once" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false"
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
110 label="Write the original A entry _once_ if _any_ overlaps found in B."
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
111 help="Just report the fact >=1 hit was found" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
112 <!-- -c -->
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
113 <param name="count" argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false"
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
114 label="For each entry in A, report the number of overlaps with B."
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
115 help="Reports 0 for A entries that have no overlap with B" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
116 <!-- -bed -->
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
117 <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false"
37
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 35
diff changeset
118 label="When using BAM input, write output as BED instead of BAM." />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
119 <!-- -sorted -g -->
37
ce3c7f062223 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
iuc
parents: 35
diff changeset
120 <expand macro="sorted" />
43
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents: 41
diff changeset
121 <expand macro="input_conditional_genome_file" optional="true" help="Only applies when used with -sorted option."/>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
122 <expand macro="print_header" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
123 </inputs>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
124 <outputs>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
125 <data name="output" format_source="inputA" metadata_source="inputA">
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
126 <change_format>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
127 <when input="bed" value="-bed" format="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
128 </change_format>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
129 </data>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
130 </outputs>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
131 <tests>
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
132 <!-- test adapted from the tutorial https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html -->
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
133 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
134 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
135 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
136 <param name="reduce_or_iterate_selector" value="iterate" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
137 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
138 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
139 <output name="output" file="intersect-default.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
140 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
141 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
142 <param name="inputA" value="intersect-query.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
143 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
144 <param name="reduce_or_iterate_selector" value="reduce" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
145 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
146 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
147 <output name="output" file="intersect-multiple.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
148 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
149 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
150 <param name="inputA" value="intersect-query.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
151 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
152 <param name="reduce_or_iterate_selector" value="reduce" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
153 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
154 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
155 <param name="overlap_mode" value="-wa,-wb" />
43
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents: 41
diff changeset
156 <param name="sorted" value="true" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
157 <output name="output" file="intersect-multiple-wa-wb.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
158 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
159 <test>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
160 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
161 <param name="inputA" value="intersect-query.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
162 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
163 <param name="reduce_or_iterate_selector" value="reduce" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
164 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
165 <param name="names" value="yes" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
166 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
167 <param name="overlap_mode" value="-wa,-wb" />
43
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents: 41
diff changeset
168 <param name="sorted" value="true" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
169 <output name="output" file="intersect-multiple-wa-wb-wnames.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
170 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
171 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
172 <param name="inputA" value="intersect-query.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
173 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
174 <param name="reduce_or_iterate_selector" value="reduce" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
175 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
176 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
177 <param name="invert" value="-v" />
43
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents: 41
diff changeset
178 <param name="sorted" value="true" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
179 <output name="output" file="intersect-multiple-invert.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
180 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
181 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
182 <param name="inputA" value="intersect-query.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
183 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
184 <param name="reduce_or_iterate_selector" value="reduce" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
185 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
186 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
187 <param name="overlap_mode" value="-wa,-wb" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
188 <conditional name="fraction_cond">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
189 <param name="fraction_select" value="specify"/>
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
190 <param name="overlap" value="1.0" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
191 </conditional>
43
07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
iuc
parents: 41
diff changeset
192 <param name="sorted" value="true" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
193 <output name="output" file="intersect-multiple-fracA.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
194 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
195 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
196 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
197 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
198 <param name="reduce_or_iterate_selector" value="iterate" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
199 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
200 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
201 <param name="overlap_mode" value="-wa" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
202 <output name="output" file="intersect-wa.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
203 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
204 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
205 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
206 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
207 <param name="reduce_or_iterate_selector" value="iterate" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
208 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
209 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
210 <param name="overlap_mode" value="-wb" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
211 <output name="output" file="intersect-wb.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
212 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
213 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
214 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
215 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
216 <param name="reduce_or_iterate_selector" value="iterate" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
217 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
218 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
219 <param name="overlap_mode" value="-wa,-wb" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
220 <output name="output" file="intersect-wa-wb.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
221 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
222 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
223 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
224 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
225 <param name="reduce_or_iterate_selector" value="iterate" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
226 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
227 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
228 <param name="overlap_mode" value="-loj" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
229 <output name="output" file="intersect-loj.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
230 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
231 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
232 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
233 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
234 <param name="reduce_or_iterate_selector" value="iterate" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
235 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
236 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
237 <param name="overlap_mode" value="-wo" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
238 <output name="output" file="intersect-wo.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
239 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
240 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
241 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
242 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
243 <param name="reduce_or_iterate_selector" value="iterate" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
244 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
245 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
246 <param name="overlap_mode" value="-wao" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
247 <output name="output" file="intersect-wao.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
248 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
249 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
250 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
251 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
252 <param name="reduce_or_iterate_selector" value="iterate" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
253 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
254 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
255 <param name="once" value="-u" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
256 <output name="output" file="intersect-unique.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
257 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
258 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
259 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
260 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
261 <param name="reduce_or_iterate_selector" value="iterate" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
262 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
263 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
264 <param name="count" value="-c"/>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
265 <output name="output" file="intersect-count.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
266 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
267 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
268 <param name="inputA" value="intersect-A.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
269 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
270 <param name="reduce_or_iterate_selector" value="iterate" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
271 <param name="inputB" value="intersect-B.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
272 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
273 <param name="invert" value="-v"/>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
274 <output name="output" file="intersect-invert.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
275 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
276 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
277 <param name="inputA" value="intersect-A2.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
278 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
279 <param name="reduce_or_iterate_selector" value="iterate" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
280 <param name="inputB" value="intersect-B2.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
281 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
282 <param name="overlap_mode" value="-wa,-wb" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
283 <conditional name="fraction_cond">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
284 <param name="fraction_select" value="specify"/>
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
285 <param name="overlap" value="0.5" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
286 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
287 <output name="output" file="intersect-fracA.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
288 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
289 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
290 <param name="inputA" value="intersect-A2.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
291 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
292 <param name="reduce_or_iterate_selector" value="iterate" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
293 <param name="inputB" value="intersect-B2.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
294 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
295 <param name="overlap_mode" value="-wa,-wb" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
296 <conditional name="fraction_cond">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
297 <param name="fraction_select" value="specify"/>
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
298 <param name="overlap" value="0.5" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
299 <conditional name="reciprocal_cond">
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
300 <param name="reciprocal" value="-r" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
301 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
302 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
303 <output name="output" file="intersect-fracA-rec.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
304 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
305 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
306 <param name="inputA" value="intersect-A2.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
307 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
308 <param name="reduce_or_iterate_selector" value="iterate" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
309 <param name="inputB" value="intersect-B2.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
310 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
311 <param name="overlap_mode" value="-wa,-wb" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
312 <conditional name="fraction_cond">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
313 <param name="fraction_select" value="specify"/>
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
314 <param name="overlap" value="0.5" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
315 <conditional name="reciprocal_cond">
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
316 <param name="overlapB" value="0.5" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
317 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
318 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
319 <output name="output" file="intersect-fracA-rec.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
320 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
321 <test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
322 <param name="inputA" value="intersect-A2.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
323 <conditional name="reduce_or_iterate">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
324 <param name="reduce_or_iterate_selector" value="iterate" />
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
325 <param name="inputB" value="intersect-B2.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
326 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
327 <param name="overlap_mode" value="-wa,-wb" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
328 <conditional name="fraction_cond">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
329 <param name="fraction_select" value="specify"/>
32
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
330 <param name="overlap" value="0.5" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
331 <conditional name="reciprocal_cond">
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
332 <param name="overlapB" value="0.5" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
333 <param name="disjoint" value="-e" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
334 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
335 </conditional>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
336 <output name="output" file="intersect-fracA.bed" ftype="bed" />
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
337 </test>
4f7a5ccd2ae9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents: 28
diff changeset
338 <!-- old tests -->
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
339 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
340 <param name="inputA" value="intersectBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
341 <param name="inputB" value="intersectBed2.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
342 <param name="overlap_mode" value="-wa" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
343 <param name="split" value="False" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
344 <output name="output" file="intersectBed_result1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
345 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
346 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
347 <param name="inputA" value="intersectBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
348 <param name="inputB" value="intersectBed2.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
349 <param name="overlap_mode" value="-wa,-wb" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
350 <param name="split" value="False" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
351 <output name="output" file="intersectBed_result2.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
352 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
353 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
354 <param name="inputA" value="intersectBed1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
355 <param name="inputB" value="intersectBed2.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
356 <param name="invert" value="True" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
357 <param name="split" value="False" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
358 <output name="output" file="intersectBed_result3.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
359 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
360 </tests>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
361 <help><![CDATA[
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
362 **What it does**
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
363
26
95a3b2c25bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
parents: 20
diff changeset
364 By far, the most common question asked of two sets of genomic features is whether or not any of the features in the two sets “overlap” with one another. This is known as feature intersection. bedtools intersect allows one to screen for overlaps between two sets of genomic features. Moreover, it allows one to have fine control as to how the intersections are reported. bedtools intersect works with both @STD_BEDTOOLS_INPUT_LABEL@ and BAM files as input.
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
365
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
366 .. image:: $PATH_TO_IMAGES/intersect-glyph.png
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
367
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
368 .. class:: infomark
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
369
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
370 Note that each BAM alignment is treated individually. Therefore, if one end of a paired-end alignment overlaps an interval in the BED file, yet the other end does not, the output file will only include the overlapping end.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
371
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
372 .. class:: infomark
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
373
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
374 Note that a BAM alignment will be sent to the output file **once** even if it overlaps more than one interval in the BED file.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
375
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
376 @REFERENCES@
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
377 ]]></help>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
378 <expand macro="citations" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
379 </tool>