Mercurial > repos > miller-lab > genome_diversity
comparison extract_primers.xml @ 17:a3af29edcce2
Uploaded Miller Lab Devshed version a51c894f5bed
author | miller-lab |
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date | Fri, 28 Sep 2012 11:57:18 -0400 |
parents | 8ae67e9fb6ff |
children | d6b961721037 |
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16:be0e2223c531 | 17:a3af29edcce2 |
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1 <tool id="gd_extract_primers" name="Pick Primers" version="1.0.0"> | |
2 <description>: Find suitable PCR primers for 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.gd_snp" ftype="gd_snp" /> | |
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 | |
49 **What it does** | |
50 | |
51 This tool extracts primers for SNPs in the dataset using the Primer3 program. | |
52 The first line of output for a given SNP reports the name of the assembled | |
53 contig, the SNP's position in the contig, the two variant nucleotides, and | |
54 Primer3's "pair penalty". The next line, if not blank, names restriction | |
55 enzymes (from the user-adjustable list) that differentially cut at that | |
56 site, but do not cut at any other position between and including the | |
57 primer positions. The next lines show the SNP's flanking regions, with | |
58 the SNP position indicated by "n", including the primer positions and an | |
59 additional 3 nucleotides. | |
60 | |
61 ----- | |
62 | |
63 **Example** | |
64 | |
65 - input file:: | |
66 | |
67 chr5_30800874_30802049 734 G A chr5 30801606 A 24 0 99 4 11 97 Y 496 0.502 0.033 0.215 6 | |
68 chr8_55117827_55119487 994 A G chr8 55118815 G 25 0 102 4 11 96 Y 22 0.502 0.025 2.365 1 | |
69 chr9_100484836_100485311 355 C T chr9 100485200 T 27 0 108 6 17 100 Y 190 0.512 0.880 2.733 4 | |
70 chr12_3635530_3637738 2101 T C chr12 3637630 T 25 0 102 4 13 93 Y 169 0.554 0.024 0.366 4 | |
71 | |
72 - output file:: | |
73 | |
74 chr5_30800874_30802049 734 G A 0.352964 | |
75 BglII,MboI,Sau3AI,Tru9I,XhoII | |
76 1 CTGAAGGTGAGCAGGATTCAGGAGACAGAAAACAAAGCCCAGGCCTGCCCAAGGTGGAAA | |
77 >>>>>>>>>>>>>>>>>>>> | |
78 | |
79 61 AGTCTAACAACTCGCCCTCTGCTTAnATCTGAGACTCACAGGGATAATAACACACTTGGT | |
80 | |
81 | |
82 21 CAAGGAATAAACTAGATATTATTCACTCCTCTAGAAGGCTGCCAGGAAAATTGCCTGACT | |
83 <<<<<<< | |
84 | |
85 181 TGAACCTTGGCTCTGA | |
86 <<<<<<<<<<<<< | |
87 etc. | |
88 | |
89 </help> | |
90 </tool> |