Mercurial > repos > iuc > bedtools

annotate bamToBed.xml @ 39:3e38c9b3214f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
author iuc
date Wed, 01 Sep 2021 11:04:15 +0000
parents fe5b4cb8356c
children 7ab85ac5f64b
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: 38
diff changeset
1 <tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy1" 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>converter</description>
39
3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
iuc
parents: 38
diff changeset
3 <expand macro="bio_tools" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
4 <macros>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
5 <import>macros.xml</import>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
6 </macros>
4
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 1
diff changeset
7 <expand macro="requirements">
27
a33db97b220c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1ec398a9421f016b852fe59d46961c12321ee5c8
iuc
parents: 4
diff changeset
8 <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
4
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 1
diff changeset
9 </expand>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
10 <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
11 <command><![CDATA[
38
fe5b4cb8356c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b822ff8f05f2396fc15bd95a71bc6878503081eb"
iuc
parents: 35
diff changeset
12 #if $input.extension in ['bam', 'unsorted.bam', 'qname_input_sorted.bam'] and $option == "-bedpe":
fe5b4cb8356c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b822ff8f05f2396fc15bd95a71bc6878503081eb"
iuc
parents: 35
diff changeset
13 samtools sort -n -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" '${input}' ./input &&
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
14 #else
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
15 ln -s '${input}' ./input.bam &&
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
16 #end if
4
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 1
diff changeset
17
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
18 bedtools bamtobed
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
19 $option
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
20 $ed_score
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
21 $split
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
22 #if $tag and str($tag).strip():
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
23 -tag '${tag}'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
24 #end if
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
25 -i ./input.bam
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
26 > '${output}'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
27 ]]></command>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
28 <inputs>
38
fe5b4cb8356c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b822ff8f05f2396fc15bd95a71bc6878503081eb"
iuc
parents: 35
diff changeset
29 <param name="input" type="data" format="unsorted.bam" label="Convert the following BAM file to BED"/>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
30 <param name="option" type="select" label="What type of BED output would you like">
4
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 1
diff changeset
31 <option value="">Create a 6-column BED file</option>
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 1
diff changeset
32 <option value="-bed12">Create a full, 12-column "blocked" BED file</option>
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 1
diff changeset
33 <option value="-bedpe">Create a paired-end, BEDPE format</option>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
34 </param>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
35 <expand macro="split" />
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
36 <param name="ed_score" argument="-ed" type="boolean" truevalue="-ed" 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
37 label="Use alignment's edit-distance for BED score" />
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
38 <param argument="-tag" type="text" optional="true"
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
39 label="Use other NUMERIC BAM alignment tag as the BED score" />
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
40 </inputs>
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
41 <outputs>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
42 <data name="output" format="bed" metadata_source="input" label="${input.name} (as BED)"/>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
43 </outputs>
1
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
44 <tests>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
45 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
46 <param name="input" value="srma_in3.bam" ftype="bam" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
47 <param name="option" value="" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
48 <param name="tag" value="" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
49 <output name="output" file="bamToBed_result1.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
50 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
51 <test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
52 <param name="input" value="srma_in3.bam" ftype="bam" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
53 <param name="option" value="" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
54 <param name="tag" value="NM" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
55 <output name="output" file="bamToBed_result2.bed" ftype="bed" />
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
56 </test>
82aac94b06c3 Uploaded
iuc
parents: 0
diff changeset
57 </tests>
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
58 <help><![CDATA[
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
59 **What it does**
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
60
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
61 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
62
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
63 .. class:: infomark
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
64
4
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 1
diff changeset
65 The "Report spliced BAM alignment..." option breaks BAM alignments with the "N" (splice) operator into distinct BED entries.
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 1
diff changeset
66 For example, using this option on a CIGAR such as 50M1000N50M would, by default, produce a single BED record that spans 1100bp.
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 1
diff changeset
67 However, using this option, it would create two separate BED records that are each 50bp in size and are separated by 1000bp (the size of the N operation).
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 1
diff changeset
68 This is important for RNA-seq and structural variation experiments.
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
69
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
70
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
71 .. class:: warningmark
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
72
4
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents: 1
diff changeset
73 If using a custom BAM alignment TAG as the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0).
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
74
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
75
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
76 @REFERENCES@
34
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 32
diff changeset
77 ]]></help>
0
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
78 <expand macro="citations" />
b8348686a0b9 Imported from capsule None
iuc
parents:
diff changeset
79 </tool>