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annotate getfastaBed.xml @ 10:c78cf6fe3018 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
author iuc
date Mon, 03 Oct 2016 07:36:08 -0400
parents 607c0576c6ab
children 7308cc546a36
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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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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" format="fasta" type="data" 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="all_fasta" />
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39 </param>
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40 </when>
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41 </conditional>
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42 <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue=""
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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 help="(-name)" />
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45 <param name="tab" type="boolean" checked="false" truevalue="-tab" falsevalue=""
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46 label="Report extract sequences in a tab-delimited format instead of in FASTA format"
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47 help="(-tab)" />
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48 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
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49 label="Force strandedness"
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50 help="If the feature occupies the antisense strand, the sequence will be reverse complemented. (-s)" />
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51 <expand macro="split" />
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52 </inputs>
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53 <outputs>
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54 <data format="fasta" name="output">
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55 <change_format>
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56 <when input="tab" value="-tab" format="tabular" />
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57 </change_format>
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58 </data>
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59 </outputs>
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60 <tests>
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61 <test>
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62 <param name="input" value="nucBed1.bed" ftype="bed" />
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63 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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64 <param name="tab" value="False" />
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65 <param name="split" value="False" />
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66 <output name="output" file="getfastaBed_result1.bed" ftype="fasta" />
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67 </test>
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68 <test>
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69 <param name="input" value="nucBed1.bed" ftype="bed" />
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70 <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
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71 <param name="tab" value="True" />
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72 <param name="split" value="False" />
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73 <output name="output" file="getfastaBed_result2.tabular" ftype="tabular" />
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74 </test>
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75 </tests>
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76 <help>
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77 <![CDATA[
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78 **What it does**
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79
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80 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
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82 .. image:: $PATH_TO_IMAGES/getfasta-glyph.png
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83
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84 .. class:: warningmark
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85
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86 1. The headers in the input FASTA file must exactly match the chromosome column in the BED file.
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87
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88 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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89
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90 @REFERENCES@
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91 ]]>
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92 </help>
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93 <expand macro="citations" />
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94 </tool>