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comparison select_snps.xml @ 12:4b6590dd7250

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author miller-lab
date Wed, 12 Sep 2012 17:10:26 -0400
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11:d4ec09e8079f 12:4b6590dd7250
1 <tool id="gd_select_snps" name="Select" version="1.0.0">
2 <description>a specified number of SNPs</description>
3
4 <command interpreter="python">
5 select_snps.py "--input=$input" "--output=$output" "--index_dir=$GALAXY_DATA_INDEX_DIR" "--num_snps=$num_snps"
6 #if $override_metadata.choice == "0":
7 "--ref_chrom_col=${input.metadata.ref}" "--ref_pos_col=${input.metadata.rPos}" "--ref_species=${input.metadata.dbkey}"
8 #else
9 "--ref_chrom_col=$ref_col" "--ref_pos_col=$rpos_col" "--ref_species=$ref_species"
10 #end if
11 </command>
12
13 <inputs>
14 <param format="tabular" name="input" type="data" label="Selected SNPS dataset">
15 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
16 </param>
17 <param name="num_snps" type="integer" value="10" optional="false" min="1" label="Number of SNPs"/>
18 <conditional name="override_metadata">
19 <param name="choice" type="select" format="integer" label="choose columns">
20 <option value="0" selected="true">No, get columns from metadata</option>
21 <option value="1" >Yes, choose columns</option>
22 </param>
23 <when value="0" />
24 <when value="1">
25 <param name="ref_col" type="data_column" data_ref="input" numerical="false" label="Column with reference chromosome"/>
26 <param name="rpos_col" type="data_column" data_ref="input" numerical="true" label="Column with reference position"/>
27 <param name="ref_species" type="select" label="Choose reference species">
28 <options from_file="gd.ref_species.txt">
29 <column name="name" index="1"/>
30 <column name="value" index="0"/>
31 </options>
32 </param>
33 </when>
34 </conditional>
35 </inputs>
36
37 <outputs>
38 <data format="gd_snp" name="output" metadata_source="input"/>
39 </outputs>
40
41 <tests>
42 <test>
43 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp"/>
44 <param name="num_snps" value="100"/>
45 <param name="choice" value="0"/>
46 <output name="output" file="test_out/select_snps/select_snps.gd_snp" />
47 </test>
48 </tests>
49
50
51 <help>
52 **What it does**
53
54 It attempts to select a specified number of SNPs from the dataset, making them
55 approximately uniformly spaced relative to the reference genome. The number
56 actually selected may be slightly more than the specified number.
57
58 -----
59
60 **Example**
61
62 - input file::
63
64 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
65 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
66 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
67 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
68 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
69 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
70 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
71 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
72 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
73 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
74 etc.
75
76 - output file::
77
78 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
79 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
80 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
81 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
82 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
83 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
84 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
85 etc.
86 </help>
87 </tool>