comparison modify_snp_table.xml @ 0:32f8fbdd754c default tip

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author rico
date Fri, 06 Apr 2012 13:59:29 -0400
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1 <tool id="gd_modify_snp_table" name="Modify" version="1.0.0">
2 <description>a SNP table</description>
3
4 <command interpreter="python">
5 modify_snp_table.py "$input" "$p1_input" "$output"
6 #if $limit_coverage.choice == "0"
7 "-1" "-1" "-1" "-1"
8 #else
9 "${limit_coverage.lo_coverage}" "${limit_coverage.hi_coverage}" "${limit_coverage.low_ind_cov}" "${limit_coverage.lo_quality}"
10 #end if
11 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
12 #set $arg = '%s:%s' % ($individual_col, $individual)
13 "$arg"
14 #end for
15 </command>
16
17 <inputs>
18 <param name="input" type="data" format="wsf" label="SNP table" />
19 <param name="p1_input" type="data" format="ind" label="Population individuals" />
20 <conditional name="limit_coverage">
21 <param name="choice" type="select" format="integer" label="Option">
22 <option value="0" selected="true">add columns to the SNP table</option>
23 <option value="1">discard some SNPs</option>
24 </param>
25 <when value="0" />
26 <when value="1">
27 <param name="lo_coverage" type="integer" min="0" value="0" label="Lower bound on total coverage" />
28 <param name="hi_coverage" type="integer" min="0" value="1000" label="Upper bound on total coverage" />
29 <param name="low_ind_cov" type="integer" min="0" value="0" label="Lower bound on individual coverage" />
30 <param name="lo_quality" type="integer" min="0" value="0" label="Lower bound on individual quality values" />
31 </when>
32 </conditional>
33 </inputs>
34
35 <outputs>
36 <data name="output" format="wsf" metadata_source="input" />
37 </outputs>
38
39 <tests>
40 <test>
41 <param name="input" value="genome_diversity/test_in/sample.wsf" ftype="wsf" />
42 <param name="p1_input" value="genome_diversity/test_in/a.ind" ftype="ind" />
43 <param name="choice" value="1" />
44 <param name="lo_coverage" value="0" />
45 <param name="hi_coverage" value="1000" />
46 <param name="low_ind_cov" value="3" />
47 <param name="lo_quality" value="30" />
48 <output name="output" file="genome_diversity/test_out/modify_snp_table/modify.wsf" />
49 </test>
50 </tests>
51
52 <help>
53 **What it does**
54
55 The user specifies that some of the individuals in the selected SNP table are
56 form a "population" that has been previously defined using the Galaxy tool to
57 select individuals from a SNP table. One option is for the program to append
58 four columns to the table, giving the total counts for the two alleles, the
59 "genotype" for the population and the maximum quality value, taken over all
60 individuals in the population. If all defined genotypes in the population
61 are 2 (agree with the reference), the population's genotype is 2; similarly
62 for 0; otherwise the genotype is 1 (unless all individuals have undefined
63 genotype, in which case it is -1. The other option is to remove rows from
64 the table for which the total coverage for the population is either too low
65 or too high, and/or if the individual coverage or quality value is too low.
66 </help>
67 </tool>