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annotate extract_flanking_dna.xml @ 31:a631c2f6d913

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Update to Miller Lab devshed revision 3c4110ffacc3
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 20 Sep 2013 13:25:27 -0400
parents d6b961721037
children
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1 <tool id="gd_extract_flanking_dna" name="Flanking Sequence" version="1.0.0">
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2 <description>: Fetch DNA sequence for intervals surrounding the given SNPs</description>
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3
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4 <command interpreter="python">
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5 extract_flanking_dna.py "--input=$input" "--output=$output" "--snps_loc=${GALAXY_DATA_INDEX_DIR}/gd.snps.loc"
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6 #if $override_metadata.choice == "0":
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7 "--scaffold_col=${input.metadata.scaffold}" "--pos_col=${input.metadata.pos}" "--species=${input.metadata.species}"
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8 #else
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9 "--scaffold_col=$scaf_col" "--pos_col=$pos_col" "--species=$species"
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10 #end if
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11 "--output_format=$output_format"
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12 </command>
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13
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14 <inputs>
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15 <param format="tabular" name="input" type="data" label="SNP dataset"/>
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16 <param name="output_format" type="select" format="integer" label="Output format">
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17 <option value="fasta" selected="true">FastA format</option>
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18 <option value="primer3">Boulder-IO (for Primer3)</option>
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19 </param>
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20 <conditional name="override_metadata">
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21 <param name="choice" type="select" format="integer" label="Choose columns" help="Datasets in gd_snp format have the columns in the metadata, all others need the columns chosen." >
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22 <option value="0" selected="true">No, get columns from metadata</option>
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23 <option value="1" >Yes, choose columns</option>
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24 </param>
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25 <when value="0" />
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26 <when value="1">
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27 <param name="scaf_col" type="data_column" data_ref="input" numerical="false" label="Column with scaffold"/>
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28 <param name="pos_col" type="data_column" data_ref="input" numerical="true" label="Column with position"/>
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29 <param name="species" type="select" label="Choose species">
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30 <options from_file="gd.species.txt">
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31 <column name="name" index="1"/>
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32 <column name="value" index="0"/>
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33 </options>
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34 </param>
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35 </when>
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36 </conditional>
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37 </inputs>
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38
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39 <outputs>
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40 <data format="txt" name="output"/>
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41 </outputs>
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42
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43 <!-- Need snpcalls files from Webb before uncommenting
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44 <tests>
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45 <test>
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46 <param name="input" value="test_out/select_snps/select_snps.gd_snp" ftype="gd_snp" />
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47 <param name="output_format" value="primer3" />
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48 <param name="choice" value="0" />
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49 <output name="output" file="test_out/extract_flanking_dna/extract_flanking_dna.txt" />
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50 </test>
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51 </tests>
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52 -->
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53
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54 <help>
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55
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56 **Dataset formats**
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57
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58 The input dataset is in tabular_ format and must contain a scaffold or
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59 chromosome column and a position column. The output is in fasta_ format or
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60 Boulder-IO_ format used by Primer3.
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61 (`Dataset missing?`_)
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62
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63 .. _tabular: ./static/formatHelp.html#tab
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64 .. _fasta: ./static/formatHelp.html#fasta
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65 .. _Boulder-IO: ./static/formatHelp.html#boulder
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66 .. _Dataset missing?: ./static/formatHelp.html
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67
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68 -----
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69
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70 **What it does**
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71
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72 This tool reports a DNA segment containing each SNP, with up to 200 nucleotides
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73 on either side of the SNP position, which is indicated by "n". Fewer nucleotides
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74 are reported if the SNP is near an end of the assembled genome fragment.
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75
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76 -----
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77
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78 **Example**
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79
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80 - input (gd_snp format)::
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81
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82 chr2_75111355_75112576 314 A C L F chr2 75111676 C F 15 4 53 2 9 48 Y 96 0.369 0.355 0.396 0
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83 chr8_93901796_93905612 2471 A C A A chr8 93904264 A A 8 0 51 10 2 14 Y 961 0.016 0.534 0.114 2
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84 chr10_7434473_7435447 524 T C S S chr10 7435005 T S 11 5 90 14 0 69 Y 626 0.066 0.406 0.727 0
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85 chr14_80021455_80022064 138 G A H H chr14 80021593 G H 14 0 69 9 6 124 Y 377 0.118 0.997 0.195 1
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86 chr15_64470252_64471048 89 G A Y Y chr15 64470341 G Y 5 6 109 14 0 69 Y 312 0.247 0.998 0.393 0
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87 chr18_48070585_48071386 514 C T E K chr18 48071100 T K 7 7 46 14 0 69 Y 2 0.200 0.032 0.163 0
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88 chr18_50154905_50155664 304 A G Y C chr18 50155208 A Y 4 2 17 5 1 22 Y 8 0.022 0.996 0.128 0
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89 chr18_57379354_57380496 315 C T V V chr18 57379669 G V 11 0 60 9 6 62 Y 726 0.118 0.048 0.014 1
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90 chr19_14240610_14242055 232 C T A V chr19 14240840 C A 18 8 56 15 5 42 Y 73 0.003 0.153 0.835 0
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91 chr19_39866997_39874915 3117 C T P P chr19 39870110 C P 3 7 65 14 2 32 Y 6 0.321 0.911 0.462 4
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92 etc.
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93
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94 - output (FastA format)::
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95
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96 > chr2_75111355_75112576 314 A C
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97 TATCTTCATTTTTATTATAGACTCTCTGAACCAATTTGCCCTGAGGCAGACTTTTTAAAGTACTGTGTAATGTATGAAGTCCTTCTGCTCAAGCAAATCATTGGCATGAAAACAGTTGCAAACTTATTGTGAGAGAAGAGTCCAAGAGTTTTAACAGTCTGTAAGTATATAGCCTGTGAGTTTGATTTCCTTCTTGTTTTTnTTCCAGAAACATGATCAGGGGCAAGTTCTATTGGATATAGTCTTCAAGCATCTTGATTTGACTGAGCGTGACTATTTTGGTTTGCAGTTGACTGACGATTCCACTGATAACCCAGTAAGTTTAAGCTGTTGTCTTTCATTGTCATTGCAATTTTTCTGTCTTTATACTAGGTCCTTTCTGATTTACATTGTTCACTGATT
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98 > chr8_93901796_93905612 2471 A C
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99 GCTGCCGCTGGATTTACTTCTGCTTGGGTCGAGAGCGGGCTGGATGGGTGAAGAGTGGGCTCCCCGGCCCCTGACCAGGCAGGTGCAGACAAGTCGGAAGAAGGCCCGCCGCATCTCCTTGCTGGCCAGCGTGTAGATGACGGGGTTCATGGCAGAGTTGAGCACGGCCAGCACGATGAACCACTGGGCCTTGAACAGGATnGCGCACTCCTTCACCTTGCAGGCCACATCCACAAGGAAAAGGATGAAGAGTGGGGACCAGCAGGCGATGAACACGCTCACCACGATCACCACGGTCCGCAGCAGGGCCATGGACCGCTCTGAGTTGTGCGGGCTGGCCACCCTGCGGCTGCTGGACTTCACCAGGAAGTAGATGCGTGCGTACAGGATCACGATGGTCAC
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100 > chr10_7434473_7435447 524 T C
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101 ATTATTAACAGAAACATTTCTTTTTCATTACCCAGGGGTTACACTGGTCGTTGATGTTAATCAGTTTTTGGAGAAGGAGAAGCAAAGTGATATTTTGTCTGTTCTGAAGCCTGCCGTTGGTAATACAAATGACGTAATCCCTGAATGTGCTGACAGGTACCATGACGCCCTGGCAAAAGCAAAAGAGCAAAAATCTAGAAGnGGTAAGCATCTTCACTGTTTAGCACAAATTAAATAGCACTTTGAATATGATGATTTCTGTGGTATTGTGTTATCTTACTTTTGAGACAAATAATCGCTTTCAAATGAATATTTCTGAATGTTTGTCATCTCTGGCAAGGAAATTTTTTAGTGTTTCTTTTCCTTTTTTGTCTTTTGGAAATCTGTGATTAACTTGGTGGC
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102 > chr14_80021455_80022064 138 G A
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103 ACCCAGGGATCAAACCCAGGTCTCCCGCATTGCAGGCGGATTCTTTACTGTCTGAGCCTCCAGGGAAGCCCTCGGGGCTGAAGGGATGGTTATGAAGGTGAGAAACAGGGGCCACCTGTCCCCAAGGTACCTTGCGACnTGCCATCTGCGCTCCACCAGTAAATGGACGTCTTCGATCCTTCTGTTGTTGGCGTAGTGCAAACGTTTGGGAAGGTGCTGTTTCAAGTAAGGCTTAAAGTGCTGGTCTGGTTTTTTACACTGAAATATAAATGGACATTGGATTTTGCAATGGAGAGTCTTCTAGAAGAGTCCAAGACATTCTCTCCAGAAAGCTGAAGG
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104 > chr15_64470252_64471048 89 G A
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105 TGTGTGTGTGTGTGTGTGTGTGTGCCTGTGTCTGTACATGCACACCACGTGGCCTCACCCAGTGCCCTCAGCTCCATGGTGATGTCCACnTAGCCGTGCTCCGCGCTGTAGTACATGGCCTCCTGGAGGGCCTTGGTGCGCGTCCGGCTCAGGCGCATGGGCCCCTCGCTGCCGCTGCCCTGGCTGGATGCATCGCTCTCTTCCACGCCCTCAGCCAGGATCTCCTCCAGGGACAGCACATCTGCTTTGGCCTGCTGTGGCTGAGTCAGGAGCTTCCTCAGGACGTTCCT
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106 etc.
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107
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108 </help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
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109 </tool>