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annotate getfastaBed.xml @ 13:fadebae7e69b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 391d2d41095edb2badf70924d3636238453ee377
author iuc
date Mon, 23 Jan 2017 06:43:06 -0500
parents 7308cc546a36
children 13400f3c3ec5
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1 <tool id="bedtools_getfastabed" name="GetFastaBed" version="@WRAPPER_VERSION@.0">
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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="requirements" />
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7 <expand macro="stdio" />
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8 <command>
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9 <![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 #end if
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15 bedtools getfasta
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16 $name
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17 $tab
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18 $strand
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19 $split
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20 -fi '$fasta_file'
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21 -bed '$input'
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22 -fo '$output'
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23 ]]>
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24 </command>
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25 <inputs>
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26 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" />
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27 <conditional name="fasta_source">
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28 <param name="fasta_source_selector" type="select" label="Choose the source for the fasta file">
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29 <option value="history" selected="True">History</option>
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30 <option value="preloaded">Server indexed files</option>
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31 </param>
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32 <when value="history">
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33 <param name="fasta" format="fasta" type="data" label="Fasta file" />
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34 </when>
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35 <when value="preloaded">
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36 <param name="fasta_id" type="select">
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37 <options from_data_table="all_fasta" />
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38 </param>
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39 </when>
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40 </conditional>
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41 <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue=""
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42 label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file"
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43 help="(-name)" />
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44 <param name="tab" type="boolean" checked="false" truevalue="-tab" falsevalue=""
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45 label="Report extract sequences in a tab-delimited format instead of in FASTA format"
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46 help="(-tab)" />
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47 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
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48 label="Force strandedness"
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49 help="If the feature occupies the antisense strand, the sequence will be reverse complemented. (-s)" />
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50 <expand macro="split" />
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51 </inputs>
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52 <outputs>
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53 <data format="fasta" name="output">
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54 <change_format>
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55 <when input="tab" value="-tab" format="tabular" />
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56 </change_format>
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57 </data>
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58 </outputs>
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59 <tests>
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60 <test>
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61 <param name="input" value="nucBed1.bed" ftype="bed" />
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62 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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63 <param name="tab" value="False" />
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64 <param name="split" value="False" />
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65 <output name="output" file="getfastaBed_result1.bed" ftype="fasta" />
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66 </test>
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67 <test>
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68 <param name="input" value="nucBed1.bed" ftype="bed" />
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69 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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70 <param name="tab" value="True" />
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71 <param name="split" value="False" />
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72 <output name="output" file="getfastaBed_result2.tabular" ftype="tabular" />
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73 </test>
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74 </tests>
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75 <help>
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76 <![CDATA[
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77 **What it does**
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78
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79 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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81 .. image:: $PATH_TO_IMAGES/getfasta-glyph.png
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82
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83 .. class:: warningmark
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84
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85 1. The headers in the input FASTA file must exactly match the chromosome column in the BED file.
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86
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87 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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88
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89 @REFERENCES@
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90 ]]>
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91 </help>
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92 <expand macro="citations" />
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93 </tool>