annotate find_intervals.xml @ 6:626b714f72bb

add gd_ploteig
author Richard Burhans <burhans@bx.psu.edu>
date Tue, 10 Apr 2012 13:51:19 -0400
parents 7a94f11fe71f
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_find_intervals" name="Find remarkable" version="1.0.0">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
2 <description>genomic intervals</description>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
3
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
4 <command interpreter="python">
4
7a94f11fe71f change output.extra_files_path to output.files_path
Richard Burhans <burhans@bx.psu.edu>
parents: 0
diff changeset
5 find_intervals.py "$input" "$input.metadata.dbkey" "$output" "$output.files_path"
0
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
6
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
7 #if $override_metadata.choice == "0"
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
8 "$input.metadata.ref" "$input.metadata.rPos"
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
9 #else
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
10 "$override_metadata.ref_col" "$override_metadata.rpos_col"
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
11 #end if
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
12
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
13 "$score_col" "$shuffles"
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
14
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
15 #if $cutoff.type == 'percentage'
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
16 "$cutoff.cutoff_pct"
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
17 #else
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
18 "=$cutoff.cutoff_val"
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
19 #end if
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
20
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
21 "$out_format"
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
22 </command>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
23
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
24 <inputs>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
25 <param name="input" type="data" format="tabular" label="Input">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
26 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
27 </param>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
28
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
29 <param name="score_col" type="data_column" data_ref="input" numerical="true" label="Column with score"/>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
30
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
31 <conditional name="cutoff">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
32 <param name="type" type="select" label="Cutoff type">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
33 <option value="percentage">percentage</option>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
34 <option value="value">value</option>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
35 </param>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
36 <when value="percentage">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
37 <param name="cutoff_pct" type="float" value="95" min="0" max="100" label="Percentage cutoff"/>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
38 </when>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
39 <when value="value">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
40 <param name="cutoff_val" type="float" value="0.0" label="Value cutoff"/>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
41 </when>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
42 </conditional>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
43
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
44 <param name="shuffles" type="integer" min="0" value="0" label="Number of randomizations"/>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
45
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
46 <param name="out_format" type="select" format="integer" label="Report SNPs">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
47 <option value="0" selected="true">No</option>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
48 <option value="1">Yes</option>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
49 </param>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
50
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
51 <conditional name="override_metadata">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
52 <param name="choice" type="select" format="integer" label="Choose columns">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
53 <option value="0" selected="true">No, get columns from metadata</option>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
54 <option value="1" >Yes, choose columns</option>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
55 </param>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
56 <when value="0" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
57 <when value="1">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
58 <param name="ref_col" type="data_column" data_ref="input" numerical="false" label="Column with reference chromosome"/>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
59 <param name="rpos_col" type="data_column" data_ref="input" numerical="true" label="Column with reference position"/>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
60 </when>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
61 </conditional>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
62 </inputs>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
63
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
64 <outputs>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
65 <data name="output" format="interval">
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
66 <change_format>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
67 <when input="out_format" value="1" format="bigwigpos" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
68 </change_format>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
69 </data>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
70 </outputs>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
71
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
72 <tests>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
73 <test>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
74 <param name="input" value="test_in/sample.wsf" ftype="wsf" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
75 <param name="score_col" value="5" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
76 <param name="type" value="value" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
77 <param name="cutoff_val" value="700.0" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
78 <param name="shuffles" value="10" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
79 <param name="out_format" value="0" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
80 <param name="choice" value="0" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
81
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
82 <output name="output" file="test_out/find_intervals/find_intervals.interval" />
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
83 </test>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
84 </tests>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
85
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
86 <help>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
87 **What it does**
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
88
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
89 The user selects a SNP table and specifies the columns containing (1)
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
90 chromosome, (2) position, (3) scores (such as an Fst-value for the SNP), (4)
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
91 a percentage or raw score for the "cutoff" and (5) the number of times the
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
92 data should be randomized (only intervals with score exceeding the maximum for
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
93 the randomized data are reported). If a percentage (e.g. 95%) is specified
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
94 for #3, then that percentile of the scores is used as the cutoff; this may
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
95 not work well if many SNPs have the same score. The program subtracts the
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
96 cutoff from every score, then finds genomic intervals (i.e., consecutive runs
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
97 of SNPs) whose total score cannot be increased by adding or subtracting one
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
98 or more SNPs at the ends of the interval.
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
99 </help>
2c498d40ecde Uploaded
miller-lab
parents:
diff changeset
100 </tool>