Mercurial > repos > xuebing > sharplabtool
comparison tools/genome_diversity/extract_primers.xml @ 0:9071e359b9a3
Uploaded
author | xuebing |
---|---|
date | Fri, 09 Mar 2012 19:37:19 -0500 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:9071e359b9a3 |
---|---|
1 <tool id="gd_extract_primers" name="Extract primers" version="1.0.0"> | |
2 <description>for selected SNPs</description> | |
3 | |
4 <command interpreter="python2.5"> | |
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 <!-- no options --> | |
22 </when> | |
23 <when value="1"> | |
24 <param name="scaf_col" type="data_column" data_ref="input" numerical="false" label="Column with scaffold"/> | |
25 <param name="pos_col" type="data_column" data_ref="input" numerical="true" label="Column with position"/> | |
26 <param name="species" type="select" label="Choose species"> | |
27 <options from_file="gd.species.txt"> | |
28 <column name="name" index="1"/> | |
29 <column name="value" index="0"/> | |
30 </options> | |
31 </param> | |
32 </when> | |
33 </conditional> | |
34 </inputs> | |
35 | |
36 <outputs> | |
37 <data format="txt" name="output"/> | |
38 </outputs> | |
39 | |
40 <tests> | |
41 <test> | |
42 <param name="input" value="gd.sample.wsf" ftype="wsf"/> | |
43 <param name="choice" value="0"/> | |
44 <output name="output" file="gd.extract_primers.txt"/> | |
45 </test> | |
46 </tests> | |
47 | |
48 | |
49 <help> | |
50 **What it does** | |
51 | |
52 This tool extracts primers for SNPs in the dataset using the Primer3 program. | |
53 The first line of output for a given SNP reports the name of the assembled | |
54 contig, the SNP's position in the contig, the two variant nucleotides, and | |
55 Primer3's "pair penalty". The next line, if not blank, names restriction | |
56 enzymes (from the user-adjustable list) that differentially cut at that | |
57 site, but do not cut at any other position between and including the | |
58 primer positions. The next lines show the SNP's flanking regions, with | |
59 the SNP position indicated by "n", including the primer positions and an | |
60 additional 3 nucleotides. | |
61 | |
62 ----- | |
63 | |
64 **Example** | |
65 | |
66 - input file:: | |
67 | |
68 chr5_30800874_30802049 734 G A chr5 30801606 A 24 0 99 4 11 97 Y 496 0.502 0.033 0.215 6 | |
69 chr8_55117827_55119487 994 A G chr8 55118815 G 25 0 102 4 11 96 Y 22 0.502 0.025 2.365 1 | |
70 chr9_100484836_100485311 355 C T chr9 100485200 T 27 0 108 6 17 100 Y 190 0.512 0.880 2.733 4 | |
71 chr12_3635530_3637738 2101 T C chr12 3637630 T 25 0 102 4 13 93 Y 169 0.554 0.024 0.366 4 | |
72 | |
73 - output file:: | |
74 | |
75 chr5_30800874_30802049 734 G A 0.352964 | |
76 BglII,MboI,Sau3AI,Tru9I,XhoII | |
77 1 CTGAAGGTGAGCAGGATTCAGGAGACAGAAAACAAAGCCCAGGCCTGCCCAAGGTGGAAA | |
78 >>>>>>>>>>>>>>>>>>>> | |
79 | |
80 61 AGTCTAACAACTCGCCCTCTGCTTAnATCTGAGACTCACAGGGATAATAACACACTTGGT | |
81 | |
82 | |
83 21 CAAGGAATAAACTAGATATTATTCACTCCTCTAGAAGGCTGCCAGGAAAATTGCCTGACT | |
84 <<<<<<< | |
85 | |
86 181 TGAACCTTGGCTCTGA | |
87 <<<<<<<<<<<<< | |
88 etc. | |
89 </help> | |
90 </tool> |