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1 <?xml version="1.0"?>
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2 <tool id="bigbed_to_fa" name="bigBedToFa" version="1.0">
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3 <description>Retrieve sequences associated with bigBed features</description>
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4
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5 <macros>
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6 <import>ucsc_macros.xml</import>
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7 </macros>
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8
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9 <expand macro="requirements_twobit">
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10 <requirement type="package" version="340">ucsc_bigbed</requirement>
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11 </expand>
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12
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13 <command detect_errors="exit_code">
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14 <![CDATA[
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15 #set no_mask = ""
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16 #if str($masking_option) == "upper":
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17 #set no_mask = "-noMask"
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18 #end if
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19
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20 ${__tool_directory__}/bigbed_to_standard_bed.pl -i "${bigbed_input}" |
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21 twoBitToFa ${no_mask} -bed=stdin "${twobit_input}" stdout
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22
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23 ## Add extra option to change soft masked bases to N's
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24 #if str($masking_option) == "hard":
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25 | awk '{ if (/^>/) { print } else { gsub(/[acgt]/, "N"); print } }'
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26 #end if
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27
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28 > "${fasta_output}"
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29 ]]>
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30 </command>
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31 <inputs>
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32 <param name="twobit_input" type="data" format="twobit" label="twoBit input file" />
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33
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34 <param name="bigbed_input" type="data" format="bigbed" label="bigBed input file" />
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35
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36 <param name="masking_option" type="select"
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37 label="Repeat masking option"
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38 help="Specify how repeats within the twoBit file should be represented">
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39
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40 <option value="upper">Show repeats in uppercase (no masking)</option>
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41
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42 <option value="lower" selected="true">Show repeats in lowercase (soft masking)</option>
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43
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44 <option value="hard">Show repeats as N's (hard masking)</option>
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45 </param>
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46
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47 </inputs>
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48 <outputs>
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49 <data name="fasta_output" format="fasta" />
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50 </outputs>
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51 <tests>
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52 <test>
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53 <!-- Test bigBedToFa with bed4 and default (soft) masking -->
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54 <param name="twobit_input" value="contigs.out.2bit" ftype="twobit" />
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55 <param name="bigbed_input" value="contigs.trf_4.bb" ftype="bigbed" />
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56 <output name="fasta_output" file="contigs.trf_4.soft.fa" />
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57 </test>
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58 <test>
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59 <!-- Test bigBedToFa with bed4 and no masking -->
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60 <param name="twobit_input" value="contigs.out.2bit" ftype="twobit" />
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61 <param name="bigbed_input" value="contigs.trf_4.bb" ftype="bigbed" />
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62 <param name="masking_option" value="upper" />
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63 <output name="fasta_output" file="contigs.trf_4.nomask.fa" />
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64 </test>
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65 <test>
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66 <!-- Test bigBedToFa with bed4 and hard masking -->
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67 <param name="twobit_input" value="contigs.out.2bit" ftype="twobit" />
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68 <param name="bigbed_input" value="contigs.trf_4.bb" ftype="bigbed" />
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69 <param name="masking_option" value="hard" />
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70 <output name="fasta_output" file="contigs.trf_4.hard.fa" />
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71 </test>
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72 <test>
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73 <!-- Test bigBedToFa with bed4+12 with default masking -->
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74 <param name="twobit_input" value="contigs.out.2bit" ftype="twobit" />
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75 <param name="bigbed_input" value="contigs.trf_4_12.bb" ftype="bigbed" />
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76 <output name="fasta_output" file="contigs.trf_4_12.fa" />
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77 </test>
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78 <test>
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79 <!-- Test bigBedToFa with bed6+2 with default masking -->
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80 <param name="twobit_input" value="contigs.out.2bit" ftype="twobit" />
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81 <param name="bigbed_input" value="contigs.models_6_2.bb" ftype="bigbed" />
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82 <output name="fasta_output" file="contigs.models_6_2.fa" />
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83 </test>
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84 <test>
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85 <!-- Test bigBedToFa with bed12+2 with default masking -->
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86 <param name="twobit_input" value="contigs.out.2bit" ftype="twobit" />
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87 <param name="bigbed_input" value="contigs.models_12_2.bb" ftype="bigbed" />
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88 <output name="fasta_output" file="contigs.models_12_2.fa" />
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89 </test>
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90 </tests>
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91 <help>
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92 <![CDATA[
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93 **What it does**
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94
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95 bigBedToFa retrieves sequences associated with the features in a
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96 `bigBed <https://genome.ucsc.edu/goldenpath/help/bigBed.html>`_ file
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97 from a `twoBit Sequence Archive <https://genome.ucsc.edu/goldenpath/help/twoBit.html>`_.
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98
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99 .. class:: infomark
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100
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101 **Extracted sequences:**
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102
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103 For files with `12 standard BED columns <https://genome.ucsc.edu/FAQ/FAQformat.html#format1>`_,
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104 this program will concatenate the sequences associated with each block (e.g., exons), and
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105 exclude the sequences between adjacent blocks (e.g., introns).
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106
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107 ]]></help>
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108
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109 <expand macro="citations" />
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110 </tool>
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