Mercurial > repos > iuc > extract_genomic_dna

annotate extract_genomic_dna.xml @ 5:c8467246b57e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 19ea4feff5ccf3744c549b9a67259947a1cb90ba
author iuc
date Sat, 21 Jan 2017 14:41:27 -0500
parents 4822a36300fd
children 53db9cb721f1
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4822a36300fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 1f61dbad440e0589e73a3bc0c304b00e9fbf2606
iuc
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1 <tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.3">
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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2 <description>using coordinates from assembled/unassembled genomes</description>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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3 <requirements>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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4 <requirement type="package" version="0.7.1">bx-python</requirement>
2
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iuc
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5 <requirement type="package" version="324">ucsc-fatotwobit</requirement>
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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6 </requirements>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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7 <command>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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8 <![CDATA[
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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9 #set genome = $input.metadata.dbkey
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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10 #set datatype = $input.datatype
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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11 mkdir -p output_dir &&
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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12 python $__tool_directory__/extract_genomic_dna.py
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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13 --input "$input"
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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14 --genome "$genome"
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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15 #if $input.is_of_type("gff"):
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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16 --input_format "gff"
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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17 --columns "1,4,5,7"
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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18 --interpret_features $interpret_features
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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19 #else:
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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20 --input_format "interval"
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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21 --columns "${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol},${input.metadata.nameCol}"
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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22 #end if
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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23 --reference_genome_source $reference_genome_cond.reference_genome_source
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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24 #if str($reference_genome_cond.reference_genome_source) == "cached"
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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25 --reference_genome $reference_genome_cond.reference_genome.fields.path
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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26 #else:
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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27 --reference_genome $reference_genome_cond.reference_genome
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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28 #end if
2
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29 --output_format $output_format_cond.output_format
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
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30 #if str($output_format_cond.output_format) == "fasta":
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
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31 --fasta_header_type $output_format_cond.fasta_header_type_cond.fasta_header_type
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
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32 #if str($output_format_cond.fasta_header_type_cond.fasta_header_type) == "char_delimited":
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33 --fasta_header_delimiter $output_format_cond.fasta_header_type_cond.fasta_header_delimiter
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
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34 #end if
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
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35 #end if
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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36 --output $output
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37 ]]>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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38 </command>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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39 <inputs>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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40 <param name="input" type="data" format="gff,interval" label="Fetch sequences for intervals in">
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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41 <validator type="unspecified_build" />
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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42 </param>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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43 <param name="interpret_features" type="select" label="Interpret features when possible" help="Applicable only when input dataset format is in the gff family">
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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44 <option value="yes">Yes</option>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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45 <option value="no">No</option>
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46 </param>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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47 <conditional name="reference_genome_cond">
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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48 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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49 <option value="cached">locally cached</option>
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50 <option value="history">from history</option>
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51 </param>
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52 <when value="cached">
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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53 <param name="reference_genome" type="select" label="Using reference genome">
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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54 <options from_data_table="twobit">
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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55 <filter type="data_meta" key="dbkey" ref="input" column="0"/>
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56 </options>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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57 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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58 </param>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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59 </when>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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60 <when value="history">
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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61 <param name="reference_genome" type="data" format="fasta" label="Using reference genome">
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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62 <options>
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63 <filter type="data_meta" key="dbkey" ref="input"/>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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64 </options>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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65 <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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66 </param>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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67 </when>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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68 </conditional>
2
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69 <conditional name="output_format_cond">
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70 <param name="output_format" type="select" label="Select output format">
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71 <option value="fasta" selected="True">fasta</option>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
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72 <option value="interval">interval</option>
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73 </param>
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74 <when value="fasta">
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75 <conditional name="fasta_header_type_cond">
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76 <param name="fasta_header_type" type="select" label="Select fasta header format">
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
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77 <option value="bedtools_getfasta_default" selected="True">bedtools getfasta default</option>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
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78 <option value="char_delimited">character delimited field values</option>
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79 </param>
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80 <when value="bedtools_getfasta_default"/>
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81 <when value="char_delimited">
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82 <param name="fasta_header_delimiter" type="select" label="Select fasta header field delimiter">
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83 <option value="underscore" selected="True">underscore (_)</option>
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84 <option value="semicolon">semicolon (;)</option>
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85 <option value="comma">comma (,)</option>
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86 <option value="tilde">tilde (~)</option>
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87 <option value="vertical_bar">vertical bar (|)</option>
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88 </param>
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89 </when>
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90 </conditional>
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91 </when>
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92 <when value="interval"/>
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93 </conditional>
0
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94 </inputs>
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95 <outputs>
1
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96 <data format_source="input" name="output" metadata_source="input">
0
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97 <change_format>
2
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98 <when input="output_format_cond.output_format" value="fasta" format="fasta" />
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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99 </change_format>
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100 </data>
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101 </outputs>
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102 <tests>
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103 <test>
2
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104 <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
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105 <param name="interpret_features" value="no"/>
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106 <param name="reference_genome_source" value="history"/>
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107 <param name="reference_genome" value="mm9.fasta"/>
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108 <param name="output_format" value="fasta"/>
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109 <param name="fasta_header_type" value="char_delimited"/>
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110 <param name="fasta_header_delimiter" value="tilde"/>
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111 <output name="output" file="extract_genomic_dna_out1.fasta" compare="contains" />
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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112 </test>
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113 <test>
2
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114 <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
0
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115 <param name="interpret_features" value="yes"/>
2
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116 <param name="reference_genome_source" value="history"/>
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117 <param name="reference_genome" value="mm9.fasta"/>
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118 <param name="output_format" value="fasta"/>
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119 <param name="fasta_header_type" value="bedtools_getfasta_default"/>
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120 <output name="output" file="extract_genomic_dna_out2.fasta" compare="contains" />
0
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121 </test>
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122 <test>
2
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123 <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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124 <param name="interpret_features" value="no"/>
2
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125 <param name="reference_genome_source" value="history"/>
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126 <param name="reference_genome" value="mm9.fasta"/>
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127 <param name="output_format" value="interval"/>
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128 <output name="output" file="extract_genomic_dna_out3.gff" compare="contains" />
0
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129 </test>
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130 <test>
2
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131 <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
0
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132 <param name="interpret_features" value="yes"/>
2
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133 <param name="reference_genome_source" value="history"/>
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134 <param name="reference_genome" value="mm9.fasta"/>
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135 <param name="output_format" value="interval"/>
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136 <output name="output" file="extract_genomic_dna_out4.gff" compare="contains" />
0
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137 </test>
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138 </tests>
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139 <help>
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140
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141 .. class:: warningmark
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142
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143 This tool requires interval or gff (special tabular formatted data). If your data is not TAB delimited, first use *Text Manipulation-&gt;Convert*.
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144
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145 .. class:: warningmark
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146
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147 Make sure that the genome build is specified for the dataset from which you are extracting sequences (click the pencil icon in the history item if it is not specified).
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148
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149 .. class:: warningmark
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150
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151 All of the following will cause a line from the input dataset to be skipped and a warning generated. The number of warnings and skipped lines is documented in the resulting history item.
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152 - Any lines that do not contain at least 3 columns, a chromosome and numerical start and end coordinates.
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153 - Sequences that fall outside of the range of a line's start and end coordinates.
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154 - Chromosome, start or end coordinates that are invalid for the specified build.
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155 - Any lines whose data columns are not separated by a **TAB** character ( other white-space characters are invalid ).
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156
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157 -----
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158
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159 **What it does**
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160
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161 This tool uses coordinate, strand, and build information to fetch genomic DNAs in FASTA or interval format.
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162
2
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163 If the output format is FASTA, the header format can be specified. Selecting the **bedtools getfasta default**
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164 option produces a FASTA header formatted like the default header produced the the bedtools getfasta tool, and
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165 the "force strandedness" option is assumed. If the input data includes a strand column and the strand is '+'
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166 or '-', it is included in the header. If the input data includes a strand column and the value is anything but
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167 '+' or '-', a '.' is included in the header. If the input data does not include a strand column, a '.' is included
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168 in the header.
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169
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170 An example FASTA header produced by selecting this option is:
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171
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172 &gt;chr7:127475281-127475310(+)
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173
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174 Selecing the **character delimited field values** option allows selection of a character delimiter that is used
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175 when generating the FASTA header with fields genome, chrom, start, end, strand (name) delimited by the
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176 selected character. For example, selecting an underscore will produce a FASTA header like this:
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177
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178 &gt;mm9_53_550_+ test_chromosome
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179
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180 while selecting a vertical bar will produce a FASTA header like this:
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181
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182 &gt;mm9|53|550|+ test_chromosome
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183
0
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184 If strand is not defined, the default value is "+".
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185
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186 -----
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187
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188 **Example**
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189
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190 If the input dataset is::
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191
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192 chr7 127475281 127475310 NM_000230 0 +
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193 chr7 127485994 127486166 NM_000230 0 +
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194 chr7 127486011 127486166 D49487 0 +
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195
2
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196 Extracting sequences with **FASTA** output data type, **character delimited field values** as header format and **header field delimiter** set to the underscore character returns::
0
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197
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198 &gt;hg17_chr7_127475281_127475310_+ NM_000230
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199 GTAGGAATCGCAGCGCCAGCGGTTGCAAG
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200 &gt;hg17_chr7_127485994_127486166_+ NM_000230
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201 GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCG
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202 GATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATC
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203 CAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAG
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204 GATCAATGACATTTCACACACG
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205 &gt;hg17_chr7_127486011_127486166_+ D49487
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206 TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGG
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207 CCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGA
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208 CACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCAC
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209 ACACG
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210
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211 Extracting sequences with **Interval** output data type returns::
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212
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213 chr7 127475281 127475310 NM_000230 0 + GTAGGAATCGCAGCGCCAGCGGTTGCAAG
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214 chr7 127485994 127486166 NM_000230 0 + GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACG
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215 chr7 127486011 127486166 D49487 0 + TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACG
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216
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217 </help>
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218 <citations>
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219 <citation type="bibtex">
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220 @unpublished{None,
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221 author = {Guru Ananda,Greg Von Kuster},
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222 title = {None},
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223 year = {None},
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224 eprint = {None},
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225 url = {http://www.bx.psu.edu/~anton/labSite/}
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226 }</citation>
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227 </citations>
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228 </tool>