Mercurial > repos > iuc > bedtools

annotate bamToBed.xml @ 64:f6c88d2e9ae5 draft default tip

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 73ebd55430874a3c1483b6dd6cce0482175482f9
author iuc
date Fri, 21 Feb 2025 21:38:34 +0000
parents 539958feb49c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
64
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
1 <tool id="bedtools_bamtobed" name="bedtools BAM to BED" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
17
a2d4c30ba2f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 8
diff changeset
2 <description>converter</description>
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
3 <macros>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
4 <import>macros.xml</import>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
5 </macros>
59
539958feb49c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
iuc
parents: 57
diff changeset
6 <expand macro="bio_tools" />
18
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
iuc
parents: 17
diff changeset
7 <expand macro="requirements">
64
f6c88d2e9ae5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
iuc
parents: 59
diff changeset
8 <requirement type="package" version="1.18">samtools</requirement>
18
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
iuc
parents: 17
diff changeset
9 </expand>
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
10 <expand macro="stdio" />
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
11 <command><![CDATA[
55
678ea22d643d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b822ff8f05f2396fc15bd95a71bc6878503081eb"
iuc
parents: 51
diff changeset
12 #if $input.extension in ['bam', 'unsorted.bam', 'qname_input_sorted.bam'] and $option == "-bedpe":
59
539958feb49c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
iuc
parents: 57
diff changeset
13 samtools sort -n -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" '${input}' > ./input.bam &&
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
14 #else
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
15 ln -s '${input}' ./input.bam &&
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
16 #end if
18
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
iuc
parents: 17
diff changeset
17
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
18 bedtools bamtobed
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
19 $option
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
20 $ed_score
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
21 $split
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
22 #if $tag and str($tag).strip():
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
23 -tag '${tag}'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
24 #end if
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
25 -i ./input.bam
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
26 > '${output}'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
27 ]]></command>
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
28 <inputs>
55
678ea22d643d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b822ff8f05f2396fc15bd95a71bc6878503081eb"
iuc
parents: 51
diff changeset
29 <param name="input" type="data" format="unsorted.bam" label="Convert the following BAM file to BED"/>
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
30 <param name="option" type="select" label="What type of BED output would you like">
18
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
iuc
parents: 17
diff changeset
31 <option value="">Create a 6-column BED file</option>
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
iuc
parents: 17
diff changeset
32 <option value="-bed12">Create a full, 12-column "blocked" BED file</option>
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
iuc
parents: 17
diff changeset
33 <option value="-bedpe">Create a paired-end, BEDPE format</option>
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
34 </param>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
35 <expand macro="split" />
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
36 <param name="ed_score" argument="-ed" type="boolean" truevalue="-ed" falsevalue="" checked="false"
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
37 label="Use alignment's edit-distance for BED score" />
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
38 <param argument="-tag" type="text" optional="true"
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
39 label="Use other NUMERIC BAM alignment tag as the BED score" />
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
40 </inputs>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
41 <outputs>
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
42 <data name="output" format="bed" metadata_source="input" label="${input.name} (as BED)"/>
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
43 </outputs>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
44 <tests>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
45 <test>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
46 <param name="input" value="srma_in3.bam" ftype="bam" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
47 <param name="option" value="" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
48 <param name="tag" value="" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
49 <output name="output" file="bamToBed_result1.bed" ftype="bed" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
50 </test>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
51 <test>
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
52 <param name="input" value="srma_in3.bam" ftype="bam" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
53 <param name="option" value="" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
54 <param name="tag" value="NM" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
55 <output name="output" file="bamToBed_result2.bed" ftype="bed" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
56 </test>
59
539958feb49c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
iuc
parents: 57
diff changeset
57 <test>
539958feb49c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
iuc
parents: 57
diff changeset
58 <param name="input" value="bedpeToBam_result1.bam" ftype="bam" />
539958feb49c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
iuc
parents: 57
diff changeset
59 <param name="option" value="-bedpe" />
539958feb49c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
iuc
parents: 57
diff changeset
60 <param name="tag" value="" />
539958feb49c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
iuc
parents: 57
diff changeset
61 <output name="output" file="bamToBed_result3.bed" ftype="bed" />
539958feb49c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
iuc
parents: 57
diff changeset
62 </test>
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
63 </tests>
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
64 <help><![CDATA[
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
65 **What it does**
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
66
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
67 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
68
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
69 .. class:: infomark
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
70
18
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
iuc
parents: 17
diff changeset
71 The "Report spliced BAM alignment..." option breaks BAM alignments with the "N" (splice) operator into distinct BED entries.
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
iuc
parents: 17
diff changeset
72 For example, using this option on a CIGAR such as 50M1000N50M would, by default, produce a single BED record that spans 1100bp.
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
iuc
parents: 17
diff changeset
73 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).
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
iuc
parents: 17
diff changeset
74 This is important for RNA-seq and structural variation experiments.
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
75
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
76
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
77 .. class:: warningmark
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
78
18
5efc48568d8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
iuc
parents: 17
diff changeset
79 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).
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
80
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
81
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
82 @REFERENCES@
50
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents: 48
diff changeset
83 ]]></help>
8
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
84 <expand macro="citations" />
0d3aa592ce27 Uploaded
iuc
parents:
diff changeset
85 </tool>