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1 <tool id="bam_to_bed_convert" name="BAM-to-BED" version="1.0"> <!-- tool's name displayed on Galaxy -->
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2 <description>converter</description>
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3
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4 <requirements> <!-- package required -->
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5 <requirement type="package" version="2.29.0">bedtools</requirement>
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6 </requirements>
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7
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8 <command interpreter="python">bamtobed.py
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9 -i $input
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10 -o $output
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11 -oot $conditional.selector
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12
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13 #if $conditional.selector =="Y":
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14 -f $conditional.format_output_chosen
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15 #end if
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16
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17 -sc $score_calcul_selector.score_calcul_BED
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18 #if $score_calcul_selector.score_calcul_BED =="tag":
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19 -tag $score_calcul_selector.calcul_BED_tag
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20 #end if
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21
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22 #if $split_boolean =="Y":
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23 -spt
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24 #end if
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25
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26 #if $cigar_boolean =="Y":
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27 -cgr
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28 #end if
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29 </command>
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30
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31
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32 <inputs>
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33
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34 <param format="bam" name="input" type="data" label="Source file"/> <!-- input file -->
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35
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36 <conditional name="conditional"> <!-- Output file format different from BED ? -->
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37 <param name="selector" type="select" label="Output file format different from BED">
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38 <option value="N">No</option>
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39 <option value="Y">Yes</option>
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40 </param>
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41
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42
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43
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44 <when value="N"/>
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45 <when value="Y"> <!-- format output chosen = not BED -->
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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 -->
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47 <option value="BEDPE">BEDPE : add fields (chrom2, star2, end2, strand2) for paired-end sequence alignments</option>
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48 <option value="BED12">BED12 : each feature is described by all 12 columns</option>
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49 </param>
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50 </when>
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51 </conditional>
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52
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53 <conditional name="score_calcul_selector"> <!-- choice of the score calculation -->
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54 <param name="score_calcul_BED" type="select" label="Select a calculation for BED score">
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55 <option value="mapq">Use mapping quality (default)</option>
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56 <option value="ed">Use alignment's edit-distance for BED score</option>
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57 <option value="tag">Use other BAM alignment tag for BED score</option>
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58 </param>
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59 <when value="tag">
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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 /!\"/>
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61 </when>
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62 </conditional>
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63
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64 <!-- option split and cigar : -->
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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>
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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>
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67
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68 </inputs>
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69
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70
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71 <outputs>
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72 <data format="bed" name="output"/>
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73 </outputs>
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74
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75
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76 <tests>
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77 <test>
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78 <param name="input" value="bam_to_bed_convert.bam"/>
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79 <output name="out_file" file="bam_to_bed_convert.bed"/>
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80 </test>
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81 </tests>
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82
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83
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84 <help>
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85 **What it does**: this tool converts sequence alignments in BAM format into BED, BED12 or BEDPE format running the command "bamtobed" of bedtools.
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86
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87 .. class:: warningmark
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88
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89 If you want a **BEDPE output**, your input has to be paired-end and sorted by read name.
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90
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91 .. class:: warningmark
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92
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93 About **score calculation** : the option "another tag" is disallowed with BEDPE output.
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94
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95 .. class:: warningmark
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96
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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.
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98
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99 .. class:: infomark
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100
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101 For more information, please refer to this link : https://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.html
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102
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103 This wrapper is available to install into other Galaxy Instances via the Galaxy
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104 Tool Shed at https://toolshed.g2.bx.psu.edu/view/geoffrey.dintilhac/bam_to_bed/68f7b5a4b1e2
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105
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106 **If you use this tool in Galaxy, please cite:**
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107
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108 </help>
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109
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110 <citations>
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111 <citation type="doi">10.1093/bioinformatics/btq033</citation>
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112 </citations>
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113
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114 </tool>
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115
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116
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