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comparison bamToBed.xml @ 4:607c0576c6ab draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
author iuc
date Wed, 27 Jan 2016 15:15:59 -0500
parents 82aac94b06c3
children a33db97b220c
comparison
equal deleted inserted replaced
3:2cd7e321d259 4:607c0576c6ab
1 <tool id="bedtools_bamtobed" name="Convert from BAM to BED" version="@WRAPPER_VERSION@.0"> 1 <tool id="bedtools_bamtobed" name="BAM to BED" version="@WRAPPER_VERSION@.0">
2 <description></description> 2 <description>converter</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements">
7 <requirement type="package" version="1.2">samtools</requirement>
8 </expand>
7 <expand macro="stdio" /> 9 <expand macro="stdio" />
8 <command> 10 <command>
9 <![CDATA[ 11 <![CDATA[
12
13 #if $input.extension == 'bam' and $option == "-bedpe":
14 samtools sort -n "${input}" ./input &&
15 #else
16 ln -s "${input}" ./input.bam &&
17 #end if
18
10 bedtools bamtobed 19 bedtools bamtobed
11 $option 20 $option
12 $ed_score 21 $ed_score
13 $split 22 $split
14 #if $tag and str($tag).strip(): 23 #if $tag and str($tag).strip():
15 -tag "${tag}" 24 -tag "${tag}"
16 #end if 25 #end if
17 -i "${input}" 26 -i ./input.bam
18 > "${output}" 27 > "${output}"
19 ]]> 28 ]]>
20 </command> 29 </command>
21 <inputs> 30 <inputs>
22 <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/> 31 <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/>
23 <param name="option" type="select" label="What type of BED output would you like"> 32 <param name="option" type="select" label="What type of BED output would you like">
24 <option value="">Create a 6-column BED file.</option> 33 <option value="">Create a 6-column BED file</option>
25 <option value="-bed12">Create a full, 12-column "blocked" BED file.</option> 34 <option value="-bed12">Create a full, 12-column "blocked" BED file</option>
26 <option value="-bedpe">Create a paired-end, BEDPE format.</option> 35 <option value="-bedpe">Create a paired-end, BEDPE format</option>
27 </param> 36 </param>
28 <expand macro="split" /> 37 <expand macro="split" />
29 <param name="ed_score" type="boolean" truevalue="-ed" falsevalue="" checked="false" 38 <param name="ed_score" type="boolean" truevalue="-ed" falsevalue="" checked="false"
30 label="Use alignment's edit-distance for BED score" /> 39 label="Use alignment's edit-distance for BED score" help="(-ed)" />
31 <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score" 40 <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"
32 help="(-tag)"/> 41 help="(-tag)"/>
33 </inputs> 42 </inputs>
34 <outputs> 43 <outputs>
35 <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/> 44 <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
54 63
55 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records. 64 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.
56 65
57 .. class:: infomark 66 .. class:: infomark
58 67
59 The "Report spliced BAM alignment..." option breaks BAM alignments with the "N" (splice) operator into distinct BED entries. For example, using this option on a CIGAR such as 50M1000N50M would, by default, produce a single BED record that spans 1100bp. 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). This is important for RNA-seq and structural variation experiments. 68 The "Report spliced BAM alignment..." option breaks BAM alignments with the "N" (splice) operator into distinct BED entries.
69 For example, using this option on a CIGAR such as 50M1000N50M would, by default, produce a single BED record that spans 1100bp.
70 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).
71 This is important for RNA-seq and structural variation experiments.
60 72
61 73
62 .. class:: warningmark 74 .. class:: warningmark
63 75
64 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). 76 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).
65 77
66 .. class:: warningmark
67
68 If creating a BEDPE output (see output formatting options), the BAM file should be sorted by query name.
69 78
70 @REFERENCES@ 79 @REFERENCES@
71 ]]> 80 ]]>
72 </help> 81 </help>
73 <expand macro="citations" /> 82 <expand macro="citations" />