Mercurial > repos > miller-lab > genome_diversity
comparison filter_gd_snp.xml @ 13:fdb4240fb565
Uploaded Miller Lab Devshed version a51c894f5bed
author | miller-lab |
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date | Fri, 28 Sep 2012 11:34:31 -0400 |
parents | |
children | f04f40a36cc8 |
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12:4b6590dd7250 | 13:fdb4240fb565 |
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1 <tool id="gd_filter_gd_snp" name="Filter SNPs" version="1.0.0"> | |
2 <description>: Discard some SNPs based on coverage or quality</description> | |
3 | |
4 <command interpreter="python"> | |
5 modify_snp_table.py "$input" "$p1_input" "$output" "$lo_coverage" "$hi_coverage" "$low_ind_cov" "$lo_quality" | |
6 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) | |
7 #set $arg = '%s:%s' % ($individual_col, $individual) | |
8 "$arg" | |
9 #end for | |
10 </command> | |
11 | |
12 <inputs> | |
13 <param name="input" type="data" format="gd_snp" label="SNP dataset" /> | |
14 <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" /> | |
15 <param name="lo_coverage" type="integer" min="0" value="0" label="Lower bound on total coverage" /> | |
16 <param name="hi_coverage" type="integer" min="0" value="1000" label="Upper bound on total coverage" /> | |
17 <param name="low_ind_cov" type="integer" min="0" value="0" label="Lower bound on individual coverage" /> | |
18 <param name="lo_quality" type="integer" min="0" value="0" label="Lower bound on individual quality values" /> | |
19 </inputs> | |
20 | |
21 <outputs> | |
22 <data name="output" format="gd_snp" metadata_source="input" /> | |
23 </outputs> | |
24 | |
25 <tests> | |
26 <test> | |
27 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" /> | |
28 <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" /> | |
29 <param name="choice" value="1" /> | |
30 <param name="lo_coverage" value="0" /> | |
31 <param name="hi_coverage" value="1000" /> | |
32 <param name="low_ind_cov" value="3" /> | |
33 <param name="lo_quality" value="30" /> | |
34 <output name="output" file="test_out/modify_snp_table/modify.gd_snp" /> | |
35 </test> | |
36 </tests> | |
37 | |
38 <help> | |
39 | |
40 **Dataset formats** | |
41 | |
42 The input datasets are in gd_snp_ and gd_indivs_ formats. | |
43 The output dataset is in gd_snp_ format. (`Dataset missing?`_) | |
44 | |
45 .. _gd_snp: ./static/formatHelp.html#gd_snp | |
46 .. _gd_indivs: ./static/formatHelp.html#gd_indivs | |
47 .. _Dataset missing?: ./static/formatHelp.html | |
48 | |
49 ----- | |
50 | |
51 **What it does** | |
52 | |
53 The user specifies that some of the individuals in a gd_snp dataset form a | |
54 "population", by supplying a list that has been previously created using the | |
55 Specify Individuals tool. SNPs are then discarded if their total coverage | |
56 for the population is too low or too high, or if their coverage or quality | |
57 score for any individual in the population is too low. | |
58 | |
59 ----- | |
60 | |
61 **Example** | |
62 | |
63 - input gd_snp:: | |
64 | |
65 Contig161_chr1_4641264_4641879 115 C T 73.5 chr1 4641382 C 6 0 2 45 8 0 2 51 15 0 2 72 5 0 2 42 6 0 2 45 10 0 2 57 Y 54 0.323 0 | |
66 Contig48_chr1_10150253_10151311 11 A G 94.3 chr1 10150264 A 1 0 2 30 1 0 2 30 1 0 2 30 3 0 2 36 1 0 2 30 1 0 2 30 Y 22 +99. 0 | |
67 Contig20_chr1_21313469_21313570 66 C T 54.0 chr1 21313534 C 4 0 2 39 4 0 2 39 5 0 2 42 4 0 2 39 4 0 2 39 5 0 2 42 N 1 +99. 0 | |
68 etc. | |
69 | |
70 - input individuals:: | |
71 | |
72 9 PB1 | |
73 13 PB2 | |
74 17 PB3 | |
75 | |
76 - output when the lower bound on individual coverage is "3":: | |
77 | |
78 Contig161_chr1_4641264_4641879 115 C T 73.5 chr1 4641382 C 6 0 2 45 8 0 2 51 15 0 2 72 5 0 2 42 6 0 2 45 10 0 2 57 Y 54 0.323 0 | |
79 Contig20_chr1_21313469_21313570 66 C T 54.0 chr1 21313534 C 4 0 2 39 4 0 2 39 5 0 2 42 4 0 2 39 4 0 2 39 5 0 2 42 N 1 +99. 0 | |
80 etc. | |
81 | |
82 </help> | |
83 </tool> |