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comparison select_snps.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
9 "--ref_chrom_col=$ref_col" "--ref_pos_col=$rpos_col" "--ref_species=$ref_species" 9 "--ref_chrom_col=$ref_col" "--ref_pos_col=$rpos_col" "--ref_species=$ref_species"
10 #end if 10 #end if
11 </command> 11 </command>
12 12
13 <inputs> 13 <inputs>
14 <param format="tabular" name="input" type="data" label="Selected SNPS dataset"> 14 <param format="tabular" name="input" type="data" label="SNP dataset">
15 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" /> 15 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
16 </param> 16 </param>
17 <param name="num_snps" type="integer" value="10" optional="false" min="1" label="Number of SNPs"/> 17 <param name="num_snps" type="integer" value="10" optional="false" min="1" label="Number of SNPs"/>
18 <conditional name="override_metadata"> 18 <conditional name="override_metadata">
19 <param name="choice" type="select" format="integer" label="choose columns"> 19 <param name="choice" type="select" format="integer" label="Choose columns" help="Datasets in gd_snp format have the column information in the metadata, all others must be chosen." >
20 <option value="0" selected="true">No, get columns from metadata</option> 20 <option value="0" selected="true">No, get columns from metadata</option>
21 <option value="1" >Yes, choose columns</option> 21 <option value="1" >Yes, choose columns</option>
22 </param> 22 </param>
23 <when value="0" /> 23 <when value="0" />
24 <when value="1"> 24 <when value="1">
48 </tests> 48 </tests>
49 49
50 50
51 <help> 51 <help>
52 52
53 **Dataset formats**
54
55 The input and output datasets are in tabular_ format.
56 (`Dataset missing?`_)
57
58 .. _tabular: ./static/formatHelp.html#tab
59 .. _Dataset missing?: ./static/formatHelp.html
60
61 -----
62
53 **What it does** 63 **What it does**
54 64
55 This tool attempts to select a specified number of SNPs from the dataset, making them 65 This tool attempts to select a specified number of SNPs from the dataset, making
56 approximately uniformly spaced relative to the reference genome. The number 66 them approximately uniformly spaced relative to the reference genome. The number
57 actually selected may be slightly more than the specified number. 67 actually selected may be slightly more than the specified number.
58 68
59 ----- 69 -----
60 70
61 **Example** 71 **Example**
62 72
63 - input file:: 73 - input (gd_snp format)::
64 74
65 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 75 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
66 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 76 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
67 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 77 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
68 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 78 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
72 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 82 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
73 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 83 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
74 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 84 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
75 etc. 85 etc.
76 86
77 - output file:: 87 - output::
78 88
79 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 89 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
80 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 90 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
81 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 91 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
82 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 92 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