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comparison bamtobed.xml @ 1:aba7a47e9ed2 draft default tip

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author geoffrey.dintilhac
date Fri, 22 Nov 2019 12:07:41 -0500
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0:c1f46404277e 1:aba7a47e9ed2
1 <tool id="bam_to_bed_convert" name="BAM-to-BED" version="1.0"> <!-- tool's name displayed on Galaxy -->
2 <description>converter</description>
3
4 <requirements> <!-- package required -->
5 <requirement type="package" version="2.29.0">bedtools</requirement>
6 </requirements>
7
8 <command interpreter="python">bamtobed.py
9 -i $input
10 -o $output
11 -oot $conditional.selector
12
13 #if $conditional.selector =="Y":
14 -f $conditional.format_output_chosen
15 #end if
16
17 -sc $score_calcul_selector.score_calcul_BED
18 #if $score_calcul_selector.score_calcul_BED =="tag":
19 -tag $score_calcul_selector.calcul_BED_tag
20 #end if
21
22 #if $split_boolean =="Y":
23 -spt
24 #end if
25
26 #if $cigar_boolean =="Y":
27 -cgr
28 #end if
29 </command>
30
31
32 <inputs>
33
34 <param format="bam" name="input" type="data" label="Source file"/> <!-- input file -->
35
36 <conditional name="conditional"> <!-- Output file format different from BED ? -->
37 <param name="selector" type="select" label="Output file format different from BED">
38 <option value="N">No</option>
39 <option value="Y">Yes</option>
40 </param>
41
42
43
44 <when value="N"/>
45 <when value="Y"> <!-- format output chosen = not BED -->
46 <param name="format_output_chosen" type="select" label="Output file format chosen" help="use BEDPE only with paired-end input (and sorted by read name) dataset"> <!-- choice of output file format -->
47 <option value="BEDPE">BEDPE : add fields (chrom2, star2, end2, strand2) for paired-end sequence alignments</option>
48 <option value="BED12">BED12 : each feature is described by all 12 columns</option>
49 </param>
50 </when>
51 </conditional>
52
53 <conditional name="score_calcul_selector"> <!-- choice of the score calculation -->
54 <param name="score_calcul_BED" type="select" label="Select a calculation for BED score">
55 <option value="mapq">Use mapping quality (default)</option>
56 <option value="ed">Use alignment's edit-distance for BED score</option>
57 <option value="tag">Use other BAM alignment tag for BED score</option>
58 </param>
59 <when value="tag">
60 <param name="calcul_BED_tag" type="text" label="Enter other BAM alignment tag as the BED score" help ="/!\ Choice of another tag for score calculation is disallowed with BEDPE output /!\"/>
61 </when>
62 </conditional>
63
64 <!-- option split and cigar : -->
65 <param name="split_boolean" type="boolean" truevalue="Y" falsevalue="N" checked="false" label="To split or not to split ?" help="Report each portion of a “split” BAM while obeying both “N” CIGAR and “D” operation. Be careful : -split is disallowed with edit-distance as a calculation for BED score."></param>
66 <param name="cigar_boolean" type="boolean" truevalue="Y" falsevalue="N" checked="false" label="CIGAR string ?" help="Add the CIGAR string to the BED entry as a 7th column. Be careful : -cigar is not displayed with -splits, and disallowed with edit-distance as a calculation for BED score."></param>
67
68 </inputs>
69
70
71 <outputs>
72 <data format="bed" name="output"/>
73 </outputs>
74
75
76 <tests>
77 <test>
78 <param name="input" value="bam_to_bed_convert.bam"/>
79 <output name="out_file" file="bam_to_bed_convert.bed"/>
80 </test>
81 </tests>
82
83
84 <help>
85 **What it does**: this tool converts sequence alignments in BAM format into BED, BED12 or BEDPE format running the command "bamtobed" of bedtools.
86
87 .. class:: warningmark
88
89 If you want a **BEDPE output**, your input has to be paired-end and sorted by read name.
90
91 .. class:: warningmark
92
93 About **score calculation** : the option "another tag" is disallowed with BEDPE output.
94
95 .. class:: warningmark
96
97 About the options **-split** and **-cigar** : -split is disallowed with edit-distance as a calculation for BED score. -cigar is not displayed with -splits, and disallowed with edit-distance as a calculation for BED score.
98
99 .. class:: infomark
100
101 For more information, please refer to this link : https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.html
102
103 This wrapper is available to install into other Galaxy Instances via the Galaxy
104 Tool Shed at
105
106 **If you use this tool in Galaxy, please cite:**
107
108 </help>
109
110 <citations>
111 <citation type="doi">10.1093/bioinformatics/btq033</citation>
112 </citations>
113
114 </tool>
115
116