annotate windowBed.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 7ab85ac5f64b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
39
3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
iuc
parents: 34
diff changeset
1 <tool id="bedtools_windowbed" name="bedtools WindowBed" version="@TOOL_VERSION@" 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 within a window around an interval</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" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
7 <expand macro="requirements" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
8 <expand macro="stdio" />
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
9 <command><![CDATA[
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
10 bedtools window
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
11 #if $inputA.is_of_type('bam'):
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
12 -abam '$inputA'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
13 #else:
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
14 -a '$inputA'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
15 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
16 -b '$inputB'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
17 $bed
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
18 $strandB
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
19 #if $addition.addition_select == 'window':
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
20 -w $addition.w
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
21 #elif $addition.addition_select == 'lr':
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
22 -l $addition.l
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
23 -r $addition.r
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
24 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
25 $original
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
26 $number
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
27 $nooverlaps
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
28 $header
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
29 > '$output'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
30 ]]></command>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
31 <inputs>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
32 <param name="inputA" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@/BAM file"/>
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
33 <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
34 <param argument="-bed" type="boolean" truevalue="-bed" 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
35 label="When using BAM input, write output as BED. The default is to write output in BAM when using a BAM file" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
36 <conditional name="addition">
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
37 <param name="addition_select" type="select" label="Choose what you want to do">
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
38 <option value="window">Add Base pairs for **both** upstream and downstream of each entry in A when searching for overlaps in B</option>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
39 <option value="lr">Add Base pairs **separately** for upstream and downstream of each entry in A when searching for overlaps in B</option>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
40 </param>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
41 <when value="window">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
42 <param argument="-w" type="integer" value="1000" label="Base pairs to add upstream and downstream" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
43 </when>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
44 <when value="lr">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
45 <param argument="-l" type="integer" value="1000"
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
46 label="Base pairs added upstream (left) of each entry in A when searching for overlaps 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
47 help="Allows one to create assymetrical “windows”. Default is 1000bp." />
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
48 <param argument="-r" type="integer" value="1000"
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
49 label="Base pairs added downstream (right) of each entry in A when searching for overlaps 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
50 help="Allows one to create assymetrical “windows”. Default is 1000bp." />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
51 </when>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
52 </conditional>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
53 <param name="strandB" type="select" label="Calculation based on strandedness?">
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
54 <option value="" selected="true">Report any hit in B</option>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
55 <option value="-sm">Only report hits in B that overlap A on the **same** strand</option>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
56 <option value="-Sm">Only report hits in B that overlap A on the **opposite** strand</option>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
57 </param>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
58 <param name="original" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false"
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
59 label="Write 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
60 help="In other words, just report the fact at least one overlap was found in B" />
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
61 <param name="number" argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false"
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
62 label="For each entry in A, report the number of hits 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
63 help="Reports 0 for A entries that have no overlap with B" />
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
64 <param name="nooverlaps" 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
65 label="Only report those entries in A that have no overlaps with B" />
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
66 <expand macro="print_header" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
67 </inputs>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
68 <outputs>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
69 <data name="output" format_source="inputA" metadata_source="inputA" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
70 </outputs>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
71 <tests>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
72 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
73 <param name="inputA" value="windowBedA.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
74 <param name="inputB" value="windowBedB.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
75 <output name="output" file="windowBed_result1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
76 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
77 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
78 <param name="inputA" value="windowBedA.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
79 <param name="inputB" value="windowBedB.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
80 <param name="addition_select" value="window" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
81 <param name="w" value="5000" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
82 <output name="output" file="windowBed_result2.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
83 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
84 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
85 <param name="inputA" value="windowBedA.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
86 <param name="inputB" value="windowBedB.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
87 <param name="addition_select" value="lr" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
88 <param name="l" value="200" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
89 <param name="r" value="20000" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
90 <output name="output" file="windowBed_result2.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
91 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
92 </tests>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
93 <help><![CDATA[
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
94 **What it does**
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
95
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
96 Similar to bedtools intersect, window searches for overlapping features in A and B. However, window adds a specified number (1000, by default) of base pairs upstream and downstream of each feature in A. In effect, this allows features in B that are “near” features in A to be detected.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
97
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
98 .. image:: $PATH_TO_IMAGES/window-glyph.png
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
99
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
100 @REFERENCES@
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
101 ]]></help>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
102 <expand macro="citations" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
103 </tool>