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annotate getfastaBed.xml @ 51:b4cf5fca8773 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:34:55 -0400
parents df28283b3778
children 7a06bb42dbb1
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1 <tool id="bedtools_getfastabed" name="bedtools GetFastaBed" version="@TOOL_VERSION@">
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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><![CDATA[
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9 #if str($fasta_source.fasta_source_selector) == 'history':
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10 #set $fasta_file = $fasta_source.fasta
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11 #else
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12 #set $fasta_file = $fasta_source.fasta_id.fields.path
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13 #end if
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14 bedtools getfasta
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15 $name
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16 $tab
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17 $strand
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18 $split
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19 -fi '$fasta_file'
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20 -bed '$input'
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21 -fo '$output'
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22 ]]></command>
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23 <inputs>
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24 <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
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25 <conditional name="fasta_source">
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26 <param name="fasta_source_selector" type="select" label="Choose the source for the FASTA file">
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27 <option value="history" selected="true">History</option>
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28 <option value="preloaded">Server indexed files</option>
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29 </param>
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30 <when value="history">
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31 <param name="fasta" argument="-fi" type="data" format="fasta" label="FASTA file" />
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32 </when>
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33 <when value="preloaded">
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34 <param name="fasta_id" type="select">
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35 <options from_data_table="fasta_indexes" />
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36 </param>
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37 </when>
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38 </conditional>
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39 <param argument="-name" type="boolean" truevalue="-name" falsevalue="" checked="false"
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40 label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file" />
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41 <param argument="-tab" type="boolean" truevalue="-tab" falsevalue="" checked="false"
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42 label="Report extract sequences in a tab-delimited format instead of in FASTA format" />
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43 <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
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44 label="Force strandedness"
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45 help="If the feature occupies the antisense strand, the sequence will be reverse complemented" />
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46 <expand macro="split" />
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47 </inputs>
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48 <outputs>
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49 <data name="output" format="fasta">
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50 <change_format>
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51 <when input="tab" value="-tab" format="tabular" />
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52 </change_format>
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53 </data>
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54 </outputs>
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55 <tests>
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56 <test>
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57 <param name="input" value="nucBed1.bed" ftype="bed" />
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58 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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59 <param name="tab" value="False" />
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60 <param name="split" value="False" />
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61 <output name="output" file="getfastaBed_result1.bed" ftype="fasta" />
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62 </test>
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63 <test>
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64 <param name="input" value="nucBed1.bed" ftype="bed" />
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65 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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66 <param name="tab" value="True" />
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67 <param name="split" value="False" />
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68 <output name="output" file="getfastaBed_result2.tabular" ftype="tabular" />
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69 </test>
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70 </tests>
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71 <help><![CDATA[
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72 **What it does**
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74 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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76 .. image:: $PATH_TO_IMAGES/getfasta-glyph.png
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78 .. class:: warningmark
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80 1. The headers in the input FASTA file must exactly match the chromosome column in the BED file.
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82 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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84 @REFERENCES@
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85 ]]></help>
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86 <expand macro="citations" />
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87 </tool>