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comparison extract_flanking_dna.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_extract_flanking_dna" name="Extract" version="1.0.0">
2 <description>DNA flanking chosen SNPs</description>
3
4 <command interpreter="python">
5 extract_flanking_dna.py "--input=$input" "--output=$output" "--snps_loc=${GALAXY_DATA_INDEX_DIR}/gd.snps.loc"
6 #if $override_metadata.choice == "0":
7 "--scaffold_col=${input.metadata.scaffold}" "--pos_col=${input.metadata.pos}" "--species=${input.metadata.species}"
8 #else
9 "--scaffold_col=$scaf_col" "--pos_col=$pos_col" "--species=$species"
10 #end if
11 "--output_format=$output_format"
12 </command>
13
14 <inputs>
15 <param format="tabular" name="input" type="data" label="Selected SNPS dataset"/>
16 <param name="output_format" type="select" format="integer" label="output format">
17 <option value="fasta" selected="true">FastA format</option>
18 <option value="primer3">Primer3 input</option>
19 </param>
20 <conditional name="override_metadata">
21 <param name="choice" type="select" format="integer" label="choose columns">
22 <option value="0" selected="true">No, get columns from metadata</option>
23 <option value="1" >Yes, choose columns</option>
24 </param>
25 <when value="0" />
26 <when value="1">
27 <param name="scaf_col" type="data_column" data_ref="input" numerical="false" label="Column with scaffold"/>
28 <param name="pos_col" type="data_column" data_ref="input" numerical="true" label="Column with position"/>
29 <param name="species" type="select" label="Choose species">
30 <options from_file="gd.species.txt">
31 <column name="name" index="1"/>
32 <column name="value" index="0"/>
33 </options>
34 </param>
35 </when>
36 </conditional>
37 </inputs>
38
39 <outputs>
40 <data format="txt" name="output"/>
41 </outputs>
42
43 <!-- Need snpcalls files from Webb before uncommenting
44 <tests>
45 <test>
46 <param name="input" value="test_out/select_snps/select_snps.gd_snp" ftype="gd_snp" />
47 <param name="output_format" value="primer3" />
48 <param name="choice" value="0" />
49 <output name="output" file="test_out/extract_flanking_dna/extract_flanking_dna.txt" />
50 </test>
51 </tests>
52 -->
53
54 <help>
55 **What it does**
56
57 It reports a DNA segment containing each SNP, with up to 200 nucleotides on
58 either side of the SNP position, which is indicated by "n". Fewer nucleotides
59 are reported if the SNP is near an end of the assembled genome fragment.
60
61 -----
62
63 **Example**
64
65 - input file::
66
67 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
68 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
69 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
70 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
71 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
72 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
73 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
74 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
75 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
76 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
77 etc.
78
79 - output file::
80
81 > chr2_75111355_75112576 314 A C
82 TATCTTCATTTTTATTATAGACTCTCTGAACCAATTTGCCCTGAGGCAGACTTTTTAAAGTACTGTGTAATGTATGAAGTCCTTCTGCTCAAGCAAATCATTGGCATGAAAACAGTTGCAAACTTATTGTGAGAGAAGAGTCCAAGAGTTTTAACAGTCTGTAAGTATATAGCCTGTGAGTTTGATTTCCTTCTTGTTTTTnTTCCAGAAACATGATCAGGGGCAAGTTCTATTGGATATAGTCTTCAAGCATCTTGATTTGACTGAGCGTGACTATTTTGGTTTGCAGTTGACTGACGATTCCACTGATAACCCAGTAAGTTTAAGCTGTTGTCTTTCATTGTCATTGCAATTTTTCTGTCTTTATACTAGGTCCTTTCTGATTTACATTGTTCACTGATT
83 > chr8_93901796_93905612 2471 A C
84 GCTGCCGCTGGATTTACTTCTGCTTGGGTCGAGAGCGGGCTGGATGGGTGAAGAGTGGGCTCCCCGGCCCCTGACCAGGCAGGTGCAGACAAGTCGGAAGAAGGCCCGCCGCATCTCCTTGCTGGCCAGCGTGTAGATGACGGGGTTCATGGCAGAGTTGAGCACGGCCAGCACGATGAACCACTGGGCCTTGAACAGGATnGCGCACTCCTTCACCTTGCAGGCCACATCCACAAGGAAAAGGATGAAGAGTGGGGACCAGCAGGCGATGAACACGCTCACCACGATCACCACGGTCCGCAGCAGGGCCATGGACCGCTCTGAGTTGTGCGGGCTGGCCACCCTGCGGCTGCTGGACTTCACCAGGAAGTAGATGCGTGCGTACAGGATCACGATGGTCAC
85 > chr10_7434473_7435447 524 T C
86 ATTATTAACAGAAACATTTCTTTTTCATTACCCAGGGGTTACACTGGTCGTTGATGTTAATCAGTTTTTGGAGAAGGAGAAGCAAAGTGATATTTTGTCTGTTCTGAAGCCTGCCGTTGGTAATACAAATGACGTAATCCCTGAATGTGCTGACAGGTACCATGACGCCCTGGCAAAAGCAAAAGAGCAAAAATCTAGAAGnGGTAAGCATCTTCACTGTTTAGCACAAATTAAATAGCACTTTGAATATGATGATTTCTGTGGTATTGTGTTATCTTACTTTTGAGACAAATAATCGCTTTCAAATGAATATTTCTGAATGTTTGTCATCTCTGGCAAGGAAATTTTTTAGTGTTTCTTTTCCTTTTTTGTCTTTTGGAAATCTGTGATTAACTTGGTGGC
87 > chr14_80021455_80022064 138 G A
88 ACCCAGGGATCAAACCCAGGTCTCCCGCATTGCAGGCGGATTCTTTACTGTCTGAGCCTCCAGGGAAGCCCTCGGGGCTGAAGGGATGGTTATGAAGGTGAGAAACAGGGGCCACCTGTCCCCAAGGTACCTTGCGACnTGCCATCTGCGCTCCACCAGTAAATGGACGTCTTCGATCCTTCTGTTGTTGGCGTAGTGCAAACGTTTGGGAAGGTGCTGTTTCAAGTAAGGCTTAAAGTGCTGGTCTGGTTTTTTACACTGAAATATAAATGGACATTGGATTTTGCAATGGAGAGTCTTCTAGAAGAGTCCAAGACATTCTCTCCAGAAAGCTGAAGG
89 > chr15_64470252_64471048 89 G A
90 TGTGTGTGTGTGTGTGTGTGTGTGCCTGTGTCTGTACATGCACACCACGTGGCCTCACCCAGTGCCCTCAGCTCCATGGTGATGTCCACnTAGCCGTGCTCCGCGCTGTAGTACATGGCCTCCTGGAGGGCCTTGGTGCGCGTCCGGCTCAGGCGCATGGGCCCCTCGCTGCCGCTGCCCTGGCTGGATGCATCGCTCTCTTCCACGCCCTCAGCCAGGATCTCCTCCAGGGACAGCACATCTGCTTTGGCCTGCTGTGGCTGAGTCAGGAGCTTCCTCAGGACGTTCCT
91 etc.
92 </help>
93 </tool>