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comparison extract_primers.xml @ 0:2c498d40ecde

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author miller-lab
date Mon, 09 Apr 2012 12:03:06 -0400
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1 <tool id="gd_extract_primers" name="Extract primers" version="1.0.0">
2 <description>for selected SNPs</description>
3
4 <command interpreter="python">
5 extract_primers.py "--input=$input" "--output=$output" "--primers_loc=${GALAXY_DATA_INDEX_DIR}/gd.primers.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 </command>
12
13 <inputs>
14 <param format="tabular" name="input" type="data" label="Selected SNPS dataset"/>
15 <conditional name="override_metadata">
16 <param name="choice" type="select" format="integer" label="choose columns">
17 <option value="0" selected="true">No, get columns from metadata</option>
18 <option value="1" >Yes, choose columns</option>
19 </param>
20 <when value="0" />
21 <when value="1">
22 <param name="scaf_col" type="data_column" data_ref="input" numerical="false" label="Column with scaffold"/>
23 <param name="pos_col" type="data_column" data_ref="input" numerical="true" label="Column with position"/>
24 <param name="species" type="select" label="Choose species">
25 <options from_file="gd.species.txt">
26 <column name="name" index="1"/>
27 <column name="value" index="0"/>
28 </options>
29 </param>
30 </when>
31 </conditional>
32 </inputs>
33
34 <outputs>
35 <data format="txt" name="output"/>
36 </outputs>
37
38 <tests>
39 <test>
40 <param name="input" value="test_out/select_snps/select_snps.wsf" ftype="wsf" />
41 <param name="choice" value="0"/>
42 <output name="output" file="test_out/extract_primers/extract_primers.txt" />
43 </test>
44 </tests>
45
46
47 <help>
48 **What it does**
49
50 This tool extracts primers for SNPs in the dataset using the Primer3 program.
51 The first line of output for a given SNP reports the name of the assembled
52 contig, the SNP's position in the contig, the two variant nucleotides, and
53 Primer3's "pair penalty". The next line, if not blank, names restriction
54 enzymes (from the user-adjustable list) that differentially cut at that
55 site, but do not cut at any other position between and including the
56 primer positions. The next lines show the SNP's flanking regions, with
57 the SNP position indicated by "n", including the primer positions and an
58 additional 3 nucleotides.
59
60 -----
61
62 **Example**
63
64 - input file::
65
66 chr5_30800874_30802049 734 G A chr5 30801606 A 24 0 99 4 11 97 Y 496 0.502 0.033 0.215 6
67 chr8_55117827_55119487 994 A G chr8 55118815 G 25 0 102 4 11 96 Y 22 0.502 0.025 2.365 1
68 chr9_100484836_100485311 355 C T chr9 100485200 T 27 0 108 6 17 100 Y 190 0.512 0.880 2.733 4
69 chr12_3635530_3637738 2101 T C chr12 3637630 T 25 0 102 4 13 93 Y 169 0.554 0.024 0.366 4
70
71 - output file::
72
73 chr5_30800874_30802049 734 G A 0.352964
74 BglII,MboI,Sau3AI,Tru9I,XhoII
75 1 CTGAAGGTGAGCAGGATTCAGGAGACAGAAAACAAAGCCCAGGCCTGCCCAAGGTGGAAA
76 >>>>>>>>>>>>>>>>>>>>
77
78 61 AGTCTAACAACTCGCCCTCTGCTTAnATCTGAGACTCACAGGGATAATAACACACTTGGT
79
80
81 21 CAAGGAATAAACTAGATATTATTCACTCCTCTAGAAGGCTGCCAGGAAAATTGCCTGACT
82 &lt;&lt;&lt;&lt;&lt;&lt;&lt;
83
84 181 TGAACCTTGGCTCTGA
85 &lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;
86 etc.
87 </help>
88 </tool>