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comparison extract_flanking_dna.xml @ 21:d6b961721037

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Miller Lab Devshed version 4c04e35b18f6
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 05 Nov 2012 12:44:17 -0500
parents 8ae67e9fb6ff
children
comparison
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20:8a4b8efbc82c 21:d6b961721037
10 #end if 10 #end if
11 "--output_format=$output_format" 11 "--output_format=$output_format"
12 </command> 12 </command>
13 13
14 <inputs> 14 <inputs>
15 <param format="tabular" name="input" type="data" label="Selected SNPS dataset"/> 15 <param format="tabular" name="input" type="data" label="SNP dataset"/>
16 <param name="output_format" type="select" format="integer" label="output format"> 16 <param name="output_format" type="select" format="integer" label="Output format">
17 <option value="fasta" selected="true">FastA format</option> 17 <option value="fasta" selected="true">FastA format</option>
18 <option value="primer3">Primer3 input</option> 18 <option value="primer3">Boulder-IO (for Primer3)</option>
19 </param> 19 </param>
20 <conditional name="override_metadata"> 20 <conditional name="override_metadata">
21 <param name="choice" type="select" format="integer" label="choose columns"> 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." >
22 <option value="0" selected="true">No, get columns from metadata</option> 22 <option value="0" selected="true">No, get columns from metadata</option>
23 <option value="1" >Yes, choose columns</option> 23 <option value="1" >Yes, choose columns</option>
24 </param> 24 </param>
25 <when value="0" /> 25 <when value="0" />
26 <when value="1"> 26 <when value="1">
51 </tests> 51 </tests>
52 --> 52 -->
53 53
54 <help> 54 <help>
55 55
56 **Dataset formats**
57
58 The input dataset is in tabular_ format and must contain a scaffold or
59 chromosome column and a position column. The output is in fasta_ format or
60 Boulder-IO_ format used by Primer3.
61 (`Dataset missing?`_)
62
63 .. _tabular: ./static/formatHelp.html#tab
64 .. _fasta: ./static/formatHelp.html#fasta
65 .. _Boulder-IO: ./static/formatHelp.html#boulder
66 .. _Dataset missing?: ./static/formatHelp.html
67
68 -----
69
56 **What it does** 70 **What it does**
57 71
58 This tool reports a DNA segment containing each SNP, with up to 200 nucleotides on 72 This tool reports a DNA segment containing each SNP, with up to 200 nucleotides
59 either side of the SNP position, which is indicated by "n". Fewer nucleotides 73 on either side of the SNP position, which is indicated by "n". Fewer nucleotides
60 are reported if the SNP is near an end of the assembled genome fragment. 74 are reported if the SNP is near an end of the assembled genome fragment.
61 75
62 ----- 76 -----
63 77
64 **Example** 78 **Example**
65 79
66 - input file:: 80 - input (gd_snp format)::
67 81
68 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 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
69 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 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
70 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 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
71 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 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
75 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 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
76 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 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
77 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 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
78 etc. 92 etc.
79 93
80 - output file:: 94 - output (FastA format)::
81 95
82 > chr2_75111355_75112576 314 A C 96 > chr2_75111355_75112576 314 A C
83 TATCTTCATTTTTATTATAGACTCTCTGAACCAATTTGCCCTGAGGCAGACTTTTTAAAGTACTGTGTAATGTATGAAGTCCTTCTGCTCAAGCAAATCATTGGCATGAAAACAGTTGCAAACTTATTGTGAGAGAAGAGTCCAAGAGTTTTAACAGTCTGTAAGTATATAGCCTGTGAGTTTGATTTCCTTCTTGTTTTTnTTCCAGAAACATGATCAGGGGCAAGTTCTATTGGATATAGTCTTCAAGCATCTTGATTTGACTGAGCGTGACTATTTTGGTTTGCAGTTGACTGACGATTCCACTGATAACCCAGTAAGTTTAAGCTGTTGTCTTTCATTGTCATTGCAATTTTTCTGTCTTTATACTAGGTCCTTTCTGATTTACATTGTTCACTGATT 97 TATCTTCATTTTTATTATAGACTCTCTGAACCAATTTGCCCTGAGGCAGACTTTTTAAAGTACTGTGTAATGTATGAAGTCCTTCTGCTCAAGCAAATCATTGGCATGAAAACAGTTGCAAACTTATTGTGAGAGAAGAGTCCAAGAGTTTTAACAGTCTGTAAGTATATAGCCTGTGAGTTTGATTTCCTTCTTGTTTTTnTTCCAGAAACATGATCAGGGGCAAGTTCTATTGGATATAGTCTTCAAGCATCTTGATTTGACTGAGCGTGACTATTTTGGTTTGCAGTTGACTGACGATTCCACTGATAACCCAGTAAGTTTAAGCTGTTGTCTTTCATTGTCATTGCAATTTTTCTGTCTTTATACTAGGTCCTTTCTGATTTACATTGTTCACTGATT
84 > chr8_93901796_93905612 2471 A C 98 > chr8_93901796_93905612 2471 A C
85 GCTGCCGCTGGATTTACTTCTGCTTGGGTCGAGAGCGGGCTGGATGGGTGAAGAGTGGGCTCCCCGGCCCCTGACCAGGCAGGTGCAGACAAGTCGGAAGAAGGCCCGCCGCATCTCCTTGCTGGCCAGCGTGTAGATGACGGGGTTCATGGCAGAGTTGAGCACGGCCAGCACGATGAACCACTGGGCCTTGAACAGGATnGCGCACTCCTTCACCTTGCAGGCCACATCCACAAGGAAAAGGATGAAGAGTGGGGACCAGCAGGCGATGAACACGCTCACCACGATCACCACGGTCCGCAGCAGGGCCATGGACCGCTCTGAGTTGTGCGGGCTGGCCACCCTGCGGCTGCTGGACTTCACCAGGAAGTAGATGCGTGCGTACAGGATCACGATGGTCAC 99 GCTGCCGCTGGATTTACTTCTGCTTGGGTCGAGAGCGGGCTGGATGGGTGAAGAGTGGGCTCCCCGGCCCCTGACCAGGCAGGTGCAGACAAGTCGGAAGAAGGCCCGCCGCATCTCCTTGCTGGCCAGCGTGTAGATGACGGGGTTCATGGCAGAGTTGAGCACGGCCAGCACGATGAACCACTGGGCCTTGAACAGGATnGCGCACTCCTTCACCTTGCAGGCCACATCCACAAGGAAAAGGATGAAGAGTGGGGACCAGCAGGCGATGAACACGCTCACCACGATCACCACGGTCCGCAGCAGGGCCATGGACCGCTCTGAGTTGTGCGGGCTGGCCACCCTGCGGCTGCTGGACTTCACCAGGAAGTAGATGCGTGCGTACAGGATCACGATGGTCAC