Mercurial > repos > iuc > bedtools

annotate getfastaBed.xml @ 45:a1a923cd89e8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit d1ee301a39e9830693eedb6ca089456081540f28
author iuc
date Thu, 02 Mar 2023 08:52:08 +0000
parents 07e8b80f278c
children 64e2edfe7a2c
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1 <tool id="bedtools_getfastabed" name="bedtools getfasta" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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2 <description>use intervals to extract sequences from a FASTA file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools" />
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <command><![CDATA[
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10 #if str($fasta_source.fasta_source_selector) == 'history':
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11 #set $fasta_file = $fasta_source.fasta
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12 #else
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13 #set $fasta_file = $fasta_source.fasta_id.fields.path
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14 ln -s '${fasta_file}.fai' 'input.fasta.fai' &&
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15 #end if
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16 ln -s '$fasta_file' 'input.fasta' &&
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17 bedtools getfasta
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18 $name
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19 $nameOnly
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20 $tab
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21 $strand
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22 $split
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23 -fi 'input.fasta'
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24 -bed '$input'
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25 -fo '$output'
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26 ]]></command>
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27 <inputs>
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28 <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
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29 <conditional name="fasta_source">
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30 <param name="fasta_source_selector" type="select" label="Choose the source for the FASTA file">
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31 <option value="history" selected="true">History</option>
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32 <option value="preloaded">Server indexed files</option>
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33 </param>
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34 <when value="history">
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35 <param name="fasta" argument="-fi" type="data" format="fasta" label="FASTA file" />
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36 </when>
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37 <when value="preloaded">
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38 <param name="fasta_id" type="select">
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39 <options from_data_table="fasta_indexes" />
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40 </param>
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41 </when>
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42 </conditional>
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43 <param argument="-name" type="boolean" truevalue="-name" falsevalue="" checked="false"
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44 label="Use the 'name' column in the BED file and the coordinates for the FASTA headers in the output FASTA file" />
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45 <param argument="-nameOnly" type="boolean" truevalue="-nameOnly" falsevalue="" checked="false"
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46 label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file" />
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47 <param argument="-tab" type="boolean" truevalue="-tab" falsevalue="" checked="false"
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48 label="Report extract sequences in a tab-delimited format instead of in FASTA format" />
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49 <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
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50 label="Force strandedness"
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51 help="If the feature occupies the antisense strand, the sequence will be reverse complemented" />
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52 <expand macro="split" />
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53 </inputs>
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54 <outputs>
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55 <data name="output" format="fasta">
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56 <change_format>
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57 <when input="tab" value="-tab" format="tabular" />
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58 </change_format>
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59 </data>
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="input" value="nucBed1.bed" ftype="bed" />
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64 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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65 <param name="tab" value="False" />
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66 <param name="split" value="False" />
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67 <param name="nameOnly" value="False" />
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68 <output name="output" file="getfastaBed_result1.bed" ftype="fasta" />
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69 </test>
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70 <test>
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71 <param name="input" value="nucBed1.bed" ftype="bed" />
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72 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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73 <param name="tab" value="True" />
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74 <param name="split" value="False" />
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75 <param name="nameOnly" value="False" />
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76 <output name="output" file="getfastaBed_result2.tabular" ftype="tabular" />
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77 </test>
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78 <test>
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79 <param name="input" value="nucBed1.bed" ftype="bed" />
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80 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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81 <param name="tab" value="False" />
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82 <param name="split" value="False" />
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83 <param name="name" value="True" />
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84 <output name="output" file="getfastaBed_result3.bed" ftype="fasta" />
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85 </test>
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86 <test>
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87 <param name="input" value="nucBed2.bed" ftype="bed" />
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88 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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89 <param name="tab" value="False" />
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90 <param name="split" value="False" />
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91 <param name="nameOnly" value="True" />
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92 <output name="output" file="getfastaBed_result4.bed" ftype="fasta" />
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93 </test>
43
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94 <test>
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95 <param name="input" value="nucBed2.bed" ftype="bed" />
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96 <param name="fasta_source_selector" value="preloaded"/>
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97 <param name="fasta_id" value="testid" />
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98 <param name="tab" value="False" />
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99 <param name="split" value="False" />
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100 <param name="nameOnly" value="True" />
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101 <output name="output" file="getfastaBed_result4.bed" ftype="fasta" />
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102 </test>
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103 </tests>
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104 <help><![CDATA[
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105 **What it does**
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106
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107 bedtools getfasta will extract the sequence defined by the coordinates in a BED interval and create a new FASTA entry in the output file for each extracted sequence. By default, the FASTA header for each extracted sequence will be formatted as follows: “>chrom>:&lt;start>-&lt;end>”.
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108
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109 .. image:: $PATH_TO_IMAGES/getfasta-glyph.png
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110
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111 .. class:: warningmark
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112
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113 1. The headers in the input FASTA file must exactly match the chromosome column in the BED file.
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114
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115 2. You can use the UNIX fold command to set the line width of the FASTA output. For example, fold -w 60 will make each line of the FASTA file have at most 60 nucleotides for easy viewing.
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116
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117 @REFERENCES@
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118 ]]></help>
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119 <expand macro="citations" />
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120 </tool>