Mercurial > repos > iuc > extract_genomic_dna

annotate extract_genomic_dna.xml @ 6:53db9cb721f1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
author iuc
date Mon, 03 Jul 2017 07:19:41 -0400
parents 4822a36300fd
children 3088e7e70888
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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>
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5 <requirement type="package" version="324">ucsc-fatotwobit</requirement>
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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>
6
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
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7 <command detect_errors="exit_code"><![CDATA[
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
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8 #set genome = $input.metadata.dbkey
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
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9 #set datatype = $input.datatype
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
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10 mkdir -p output_dir &&
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
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11 python '$__tool_directory__/extract_genomic_dna.py'
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
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12 --input '$input'
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
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13 --genome '$genome'
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
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14 #if $input.is_of_type("gff"):
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
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15 --input_format gff
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
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16 --columns '1,4,5,7'
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
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17 --interpret_features $interpret_features
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
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18 #else:
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
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19 --input_format interval
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
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20 --columns '${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol},${input.metadata.nameCol}'
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
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21 #end if
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
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22 --reference_genome_source $reference_genome_cond.reference_genome_source
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
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23 #if str($reference_genome_cond.reference_genome_source) == "cached"
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
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24 --reference_genome '$reference_genome_cond.reference_genome.fields.path'
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
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25 #else:
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
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26 --reference_genome '$reference_genome_cond.reference_genome'
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
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27 #end if
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
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28 --output_format $output_format_cond.output_format
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
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29 #if str($output_format_cond.output_format) == "fasta":
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
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30 --fasta_header_type $output_format_cond.fasta_header_type_cond.fasta_header_type
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
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31 #if str($output_format_cond.fasta_header_type_cond.fasta_header_type) == "char_delimited":
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
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32 --fasta_header_delimiter $output_format_cond.fasta_header_type_cond.fasta_header_delimiter
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
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33 #end if
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
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34 #end if
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
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35 --output '$output'
0
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36 ]]>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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37 </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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38 <inputs>
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39 <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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40 <validator type="unspecified_build" />
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41 </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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42 <param name="interpret_features" type="select" label="Interpret features when possible" help="Applicable only when input dataset format is in the gff family">
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43 <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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44 <option value="no">No</option>
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45 </param>
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46 <conditional name="reference_genome_cond">
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47 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
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48 <option value="cached">locally cached</option>
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49 <option value="history">from history</option>
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50 </param>
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51 <when value="cached">
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52 <param name="reference_genome" type="select" label="Using reference genome">
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53 <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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54 <filter type="data_meta" key="dbkey" ref="input" column="0"/>
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55 </options>
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56 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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57 </param>
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58 </when>
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59 <when value="history">
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60 <param name="reference_genome" type="data" format="fasta" label="Using reference genome">
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61 <options>
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62 <filter type="data_meta" key="dbkey" ref="input"/>
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63 </options>
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64 <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/>
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65 </param>
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66 </when>
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67 </conditional>
2
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68 <conditional name="output_format_cond">
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69 <param name="output_format" type="select" label="Select output format">
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70 <option value="fasta" selected="True">fasta</option>
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71 <option value="interval">interval</option>
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72 </param>
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73 <when value="fasta">
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74 <conditional name="fasta_header_type_cond">
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75 <param name="fasta_header_type" type="select" label="Select fasta header format">
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76 <option value="bedtools_getfasta_default" selected="True">bedtools getfasta default</option>
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77 <option value="char_delimited">character delimited field values</option>
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78 </param>
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79 <when value="bedtools_getfasta_default"/>
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80 <when value="char_delimited">
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81 <param name="fasta_header_delimiter" type="select" label="Select fasta header field delimiter">
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82 <option value="underscore" selected="True">underscore (_)</option>
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83 <option value="semicolon">semicolon (;)</option>
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84 <option value="comma">comma (,)</option>
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85 <option value="tilde">tilde (~)</option>
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86 <option value="vertical_bar">vertical bar (|)</option>
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87 </param>
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88 </when>
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89 </conditional>
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90 </when>
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91 <when value="interval"/>
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92 </conditional>
0
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93 </inputs>
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94 <outputs>
1
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95 <data format_source="input" name="output" metadata_source="input">
0
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96 <change_format>
2
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97 <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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98 </change_format>
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99 </data>
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100 </outputs>
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101 <tests>
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102 <test>
2
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103 <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
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104 <param name="interpret_features" value="no"/>
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105 <param name="reference_genome_source" value="history"/>
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106 <param name="reference_genome" value="mm9.fasta"/>
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107 <param name="output_format" value="fasta"/>
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108 <param name="fasta_header_type" value="char_delimited"/>
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109 <param name="fasta_header_delimiter" value="tilde"/>
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110 <output name="output" file="extract_genomic_dna_out1.fasta" compare="contains" />
0
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111 </test>
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112 <test>
2
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113 <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
0
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114 <param name="interpret_features" value="yes"/>
2
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115 <param name="reference_genome_source" value="history"/>
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116 <param name="reference_genome" value="mm9.fasta"/>
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117 <param name="output_format" value="fasta"/>
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118 <param name="fasta_header_type" value="bedtools_getfasta_default"/>
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119 <output name="output" file="extract_genomic_dna_out2.fasta" compare="contains" />
0
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120 </test>
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121 <test>
2
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122 <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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123 <param name="interpret_features" value="no"/>
2
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124 <param name="reference_genome_source" value="history"/>
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125 <param name="reference_genome" value="mm9.fasta"/>
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126 <param name="output_format" value="interval"/>
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127 <output name="output" file="extract_genomic_dna_out3.gff" compare="contains" />
0
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128 </test>
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129 <test>
2
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130 <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
0
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131 <param name="interpret_features" value="yes"/>
2
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132 <param name="reference_genome_source" value="history"/>
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133 <param name="reference_genome" value="mm9.fasta"/>
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134 <param name="output_format" value="interval"/>
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135 <output name="output" file="extract_genomic_dna_out4.gff" compare="contains" />
0
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136 </test>
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137 </tests>
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138 <help>
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139
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140 .. class:: warningmark
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141
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142 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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143
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144 .. class:: warningmark
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145
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146 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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147
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148 .. class:: warningmark
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149
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150 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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151 - Any lines that do not contain at least 3 columns, a chromosome and numerical start and end coordinates.
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152 - Sequences that fall outside of the range of a line's start and end coordinates.
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153 - Chromosome, start or end coordinates that are invalid for the specified build.
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154 - Any lines whose data columns are not separated by a **TAB** character ( other white-space characters are invalid ).
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155
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156 -----
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157
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158 **What it does**
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159
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160 This tool uses coordinate, strand, and build information to fetch genomic DNAs in FASTA or interval format.
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161
2
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162 If the output format is FASTA, the header format can be specified. Selecting the **bedtools getfasta default**
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163 option produces a FASTA header formatted like the default header produced the the bedtools getfasta tool, and
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164 the "force strandedness" option is assumed. If the input data includes a strand column and the strand is '+'
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165 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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166 '+' or '-', a '.' is included in the header. If the input data does not include a strand column, a '.' is included
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167 in the header.
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168
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169 An example FASTA header produced by selecting this option is:
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170
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171 &gt;chr7:127475281-127475310(+)
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172
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173 Selecing the **character delimited field values** option allows selection of a character delimiter that is used
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174 when generating the FASTA header with fields genome, chrom, start, end, strand (name) delimited by the
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175 selected character. For example, selecting an underscore will produce a FASTA header like this:
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176
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177 &gt;mm9_53_550_+ test_chromosome
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178
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179 while selecting a vertical bar will produce a FASTA header like this:
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180
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181 &gt;mm9|53|550|+ test_chromosome
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182
0
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183 If strand is not defined, the default value is "+".
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184
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185 -----
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186
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187 **Example**
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188
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189 If the input dataset is::
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190
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191 chr7 127475281 127475310 NM_000230 0 +
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192 chr7 127485994 127486166 NM_000230 0 +
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193 chr7 127486011 127486166 D49487 0 +
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194
2
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195 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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196
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197 &gt;hg17_chr7_127475281_127475310_+ NM_000230
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198 GTAGGAATCGCAGCGCCAGCGGTTGCAAG
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199 &gt;hg17_chr7_127485994_127486166_+ NM_000230
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200 GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCG
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201 GATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATC
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202 CAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAG
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203 GATCAATGACATTTCACACACG
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204 &gt;hg17_chr7_127486011_127486166_+ D49487
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205 TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGG
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206 CCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGA
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207 CACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCAC
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208 ACACG
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209
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210 Extracting sequences with **Interval** output data type returns::
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211
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212 chr7 127475281 127475310 NM_000230 0 + GTAGGAATCGCAGCGCCAGCGGTTGCAAG
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213 chr7 127485994 127486166 NM_000230 0 + GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACG
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214 chr7 127486011 127486166 D49487 0 + TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACG
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215
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216 </help>
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217 <citations>
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218 <citation type="bibtex">
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219 @unpublished{None,
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220 author = {Guru Ananda,Greg Von Kuster},
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221 title = {None},
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222 year = {None},
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223 eprint = {None},
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224 url = {http://www.bx.psu.edu/~anton/labSite/}
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225 }</citation>
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226 </citations>
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227 </tool>