annotate modify_snp_table.xml @ 1:0df7a9b89f13

add empty snifffers section to mitigate toolshed bug; new version of dpmix
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 09 Apr 2012 12:40:57 -0400
parents 2c498d40ecde
children e29f4d801bb0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
1 <tool id="gd_modify_snp_table" name="Modify" version="1.0.0">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
2 <description>a SNP table</description>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
3
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
4 <command interpreter="python">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
5 modify_snp_table.py "$input" "$p1_input" "$output"
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
6 #if $limit_coverage.choice == "0"
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
7 "-1" "-1" "-1" "-1"
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
8 #else
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
9 "${limit_coverage.lo_coverage}" "${limit_coverage.hi_coverage}" "${limit_coverage.low_ind_cov}" "${limit_coverage.lo_quality}"
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
10 #end if
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
11 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
12 #set $arg = '%s:%s' % ($individual_col, $individual)
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
13 "$arg"
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
14 #end for
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
15 </command>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
16
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
17 <inputs>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
18 <param name="input" type="data" format="wsf" label="SNP table" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
19 <param name="p1_input" type="data" format="ind" label="Population individuals" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
20 <conditional name="limit_coverage">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
21 <param name="choice" type="select" format="integer" label="Option">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
22 <option value="0" selected="true">add columns to the SNP table</option>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
23 <option value="1">discard some SNPs</option>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
24 </param>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
25 <when value="0" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
26 <when value="1">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
27 <param name="lo_coverage" type="integer" min="0" value="0" label="Lower bound on total coverage" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
28 <param name="hi_coverage" type="integer" min="0" value="1000" label="Upper bound on total coverage" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
29 <param name="low_ind_cov" type="integer" min="0" value="0" label="Lower bound on individual coverage" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
30 <param name="lo_quality" type="integer" min="0" value="0" label="Lower bound on individual quality values" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
31 </when>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
32 </conditional>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
33 </inputs>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
34
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
35 <outputs>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
36 <data name="output" format="wsf" metadata_source="input" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
37 </outputs>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
38
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
39 <tests>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
40 <test>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
41 <param name="input" value="test_in/sample.wsf" ftype="wsf" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
42 <param name="p1_input" value="test_in/a.ind" ftype="ind" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
43 <param name="choice" value="1" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
44 <param name="lo_coverage" value="0" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
45 <param name="hi_coverage" value="1000" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
46 <param name="low_ind_cov" value="3" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
47 <param name="lo_quality" value="30" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
48 <output name="output" file="test_out/modify_snp_table/modify.wsf" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
49 </test>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
50 </tests>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
51
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
52 <help>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
53 **What it does**
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
54
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
55 The user specifies that some of the individuals in the selected SNP table are
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
56 form a "population" that has been previously defined using the Galaxy tool to
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
57 select individuals from a SNP table. One option is for the program to append
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
58 four columns to the table, giving the total counts for the two alleles, the
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
59 "genotype" for the population and the maximum quality value, taken over all
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
60 individuals in the population. If all defined genotypes in the population
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
61 are 2 (agree with the reference), the population's genotype is 2; similarly
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
62 for 0; otherwise the genotype is 1 (unless all individuals have undefined
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
63 genotype, in which case it is -1. The other option is to remove rows from
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
64 the table for which the total coverage for the population is either too low
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
65 or too high, and/or if the individual coverage or quality value is too low.
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
66 </help>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
67 </tool>