Mercurial > repos > iuc > bedtools

annotate getfastaBed.xml @ 40:a68aa6c1204a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 29bd1be4655cd26052095a49a8e188d2572b703b"
author iuc
date Thu, 09 Sep 2021 13:04:07 +0000
parents 3e38c9b3214f
children 7ab85ac5f64b
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3e38c9b3214f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
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1 <tool id="bedtools_getfastabed" name="bedtools GetFastaBed" version="@TOOL_VERSION@" profile="@PROFILE@">
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2 <description>use intervals to extract sequences from a FASTA file</description>
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3 <expand macro="bio_tools" />
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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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 $tab
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20 $strand
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21 $split
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22 -fi 'input.fasta'
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23 -bed '$input'
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24 -fo '$output'
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25 ]]></command>
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26 <inputs>
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27 <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
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28 <conditional name="fasta_source">
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29 <param name="fasta_source_selector" type="select" label="Choose the source for the FASTA file">
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30 <option value="history" selected="true">History</option>
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31 <option value="preloaded">Server indexed files</option>
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32 </param>
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33 <when value="history">
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34 <param name="fasta" argument="-fi" type="data" format="fasta" label="FASTA file" />
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35 </when>
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36 <when value="preloaded">
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37 <param name="fasta_id" type="select">
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38 <options from_data_table="fasta_indexes" />
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39 </param>
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40 </when>
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41 </conditional>
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42 <param argument="-name" type="boolean" truevalue="-name" falsevalue="" checked="false"
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43 label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file" />
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44 <param argument="-tab" type="boolean" truevalue="-tab" falsevalue="" checked="false"
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45 label="Report extract sequences in a tab-delimited format instead of in FASTA format" />
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46 <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
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47 label="Force strandedness"
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48 help="If the feature occupies the antisense strand, the sequence will be reverse complemented" />
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49 <expand macro="split" />
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50 </inputs>
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51 <outputs>
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52 <data name="output" format="fasta">
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53 <change_format>
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54 <when input="tab" value="-tab" format="tabular" />
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55 </change_format>
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56 </data>
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="input" value="nucBed1.bed" ftype="bed" />
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61 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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62 <param name="tab" value="False" />
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63 <param name="split" value="False" />
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64 <output name="output" file="getfastaBed_result1.bed" ftype="fasta" />
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65 </test>
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66 <test>
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67 <param name="input" value="nucBed1.bed" ftype="bed" />
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68 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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69 <param name="tab" value="True" />
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70 <param name="split" value="False" />
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71 <output name="output" file="getfastaBed_result2.tabular" ftype="tabular" />
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72 </test>
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73 </tests>
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74 <help><![CDATA[
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75 **What it does**
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76
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77 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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79 .. image:: $PATH_TO_IMAGES/getfasta-glyph.png
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80
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81 .. class:: warningmark
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82
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83 1. The headers in the input FASTA file must exactly match the chromosome column in the BED file.
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84
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85 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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86
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87 @REFERENCES@
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88 ]]></help>
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89 <expand macro="citations" />
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90 </tool>