|
0
|
1 <tool id="gd_find_intervals" name="Find remarkable" version="1.0.0">
|
|
|
2 <description>genomic intervals</description>
|
|
|
3
|
|
|
4 <command interpreter="python">
|
|
|
5 find_intervals.py "$input" "$input.metadata.dbkey" "$output" "$output.extra_files_path"
|
|
|
6
|
|
|
7 #if $override_metadata.choice == "0"
|
|
|
8 "$input.metadata.ref" "$input.metadata.rPos"
|
|
|
9 #else
|
|
|
10 "$override_metadata.ref_col" "$override_metadata.rpos_col"
|
|
|
11 #end if
|
|
|
12
|
|
|
13 "$score_col" "$shuffles"
|
|
|
14
|
|
|
15 #if $cutoff.type == 'percentage'
|
|
|
16 "$cutoff.cutoff_pct"
|
|
|
17 #else
|
|
|
18 "=$cutoff.cutoff_val"
|
|
|
19 #end if
|
|
|
20
|
|
|
21 "$out_format"
|
|
|
22 </command>
|
|
|
23
|
|
|
24 <inputs>
|
|
|
25 <param name="input" type="data" format="tabular" label="Input">
|
|
|
26 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
|
|
|
27 </param>
|
|
|
28
|
|
|
29 <param name="score_col" type="data_column" data_ref="input" numerical="true" label="Column with score"/>
|
|
|
30
|
|
|
31 <conditional name="cutoff">
|
|
|
32 <param name="type" type="select" label="Cutoff type">
|
|
|
33 <option value="percentage">percentage</option>
|
|
|
34 <option value="value">value</option>
|
|
|
35 </param>
|
|
|
36 <when value="percentage">
|
|
|
37 <param name="cutoff_pct" type="float" value="95" min="0" max="100" label="Percentage cutoff"/>
|
|
|
38 </when>
|
|
|
39 <when value="value">
|
|
|
40 <param name="cutoff_val" type="float" value="0.0" label="Value cutoff"/>
|
|
|
41 </when>
|
|
|
42 </conditional>
|
|
|
43
|
|
|
44 <param name="shuffles" type="integer" min="0" value="0" label="Number of randomizations"/>
|
|
|
45
|
|
|
46 <param name="out_format" type="select" format="integer" label="Report SNPs">
|
|
|
47 <option value="0" selected="true">No</option>
|
|
|
48 <option value="1">Yes</option>
|
|
|
49 </param>
|
|
|
50
|
|
|
51 <conditional name="override_metadata">
|
|
|
52 <param name="choice" type="select" format="integer" label="Choose columns">
|
|
|
53 <option value="0" selected="true">No, get columns from metadata</option>
|
|
|
54 <option value="1" >Yes, choose columns</option>
|
|
|
55 </param>
|
|
|
56 <when value="0" />
|
|
|
57 <when value="1">
|
|
|
58 <param name="ref_col" type="data_column" data_ref="input" numerical="false" label="Column with reference chromosome"/>
|
|
|
59 <param name="rpos_col" type="data_column" data_ref="input" numerical="true" label="Column with reference position"/>
|
|
|
60 </when>
|
|
|
61 </conditional>
|
|
|
62 </inputs>
|
|
|
63
|
|
|
64 <outputs>
|
|
|
65 <data name="output" format="interval">
|
|
|
66 <change_format>
|
|
|
67 <when input="out_format" value="1" format="bigwigpos" />
|
|
|
68 </change_format>
|
|
|
69 </data>
|
|
|
70 </outputs>
|
|
|
71
|
|
|
72 <tests>
|
|
|
73 <test>
|
|
|
74 <param name="input" value="genome_diversity/test_in/sample.wsf" ftype="wsf" />
|
|
|
75 <param name="score_col" value="5" />
|
|
|
76 <param name="type" value="value" />
|
|
|
77 <param name="cutoff_val" value="700.0" />
|
|
|
78 <param name="shuffles" value="10" />
|
|
|
79 <param name="out_format" value="0" />
|
|
|
80 <param name="choice" value="0" />
|
|
|
81
|
|
|
82 <output name="output" file="genome_diversity/test_out/find_intervals/find_intervals.interval" />
|
|
|
83 </test>
|
|
|
84 </tests>
|
|
|
85
|
|
|
86 <help>
|
|
|
87 **What it does**
|
|
|
88
|
|
|
89 The user selects a SNP table and specifies the columns containing (1)
|
|
|
90 chromosome, (2) position, (3) scores (such as an Fst-value for the SNP), (4)
|
|
|
91 a percentage or raw score for the "cutoff" and (5) the number of times the
|
|
|
92 data should be randomized (only intervals with score exceeding the maximum for
|
|
|
93 the randomized data are reported). If a percentage (e.g. 95%) is specified
|
|
|
94 for #3, then that percentile of the scores is used as the cutoff; this may
|
|
|
95 not work well if many SNPs have the same score. The program subtracts the
|
|
|
96 cutoff from every score, then finds genomic intervals (i.e., consecutive runs
|
|
|
97 of SNPs) whose total score cannot be increased by adding or subtracting one
|
|
|
98 or more SNPs at the ends of the interval.
|
|
|
99 </help>
|
|
|
100 </tool>
|
