Mercurial > repos > miller-lab > genome_diversity

annotate find_intervals.xml @ 37:884ccb07885b

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fixed output_id
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 16:43:43 -0500
parents a631c2f6d913
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
22
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents: 21
diff changeset
1 <tool id="gd_find_intervals" name="Remarkable Intervals" version="1.1.0">
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
2 <description>: Find high-scoring runs of SNPs</description>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
3
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
4 <command interpreter="python">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
5 find_intervals.py "$input" "$input.metadata.dbkey" "$output" "$output.files_path"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
6
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
7 #if $override_metadata.choice == "0"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
8 "$input.metadata.ref" "$input.metadata.rPos"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
9 #else
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
10 "$override_metadata.ref_col" "$override_metadata.rpos_col"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
11 #end if
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
12
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
13 "$score_col" "$shuffles"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
15 #if $cutoff.type == 'percentage'
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
16 "$cutoff.cutoff_pct"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
17 #else
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
18 "=$cutoff.cutoff_val"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
19 #end if
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
20
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
21 "$out_format"
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
22 </command>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
23
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
24 <inputs>
21
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
25 <param name="input" type="data" format="tabular" label="Dataset">
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
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" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
27 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
28
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
29 <param name="score_col" type="data_column" data_ref="input" numerical="true" label="Column with score"/>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
30
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
31 <conditional name="cutoff">
21
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
32 <param name="type" type="select" label="Score-shift type">
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
33 <option value="percentage">percentage</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
34 <option value="value">value</option>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
35 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
36 <when value="percentage">
21
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
37 <param name="cutoff_pct" type="float" value="95" min="0" max="100" label="Percentage score-shift"/>
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
38 </when>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
39 <when value="value">
21
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
40 <param name="cutoff_val" type="float" value="0.0" label="Value score-shift"/>
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
41 </when>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
42 </conditional>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
43
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
44 <param name="shuffles" type="integer" min="0" value="0" label="Number of randomizations"/>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
45
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
46 <param name="out_format" type="select" format="integer" label="Report individual positions">
21
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
47 <option value="0" selected="true">no</option>
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
48 <option value="1">yes</option>
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
49 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
50
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
51 <conditional name="override_metadata">
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
52 <param name="choice" type="select" format="integer" label="Choose columns" help="Note: you must choose the columns if the input dataset is neither gd_snp nor gd_genotype.">
21
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
53 <option value="0" selected="true">no, get columns from metadata</option>
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
54 <option value="1" >yes, choose columns here</option>
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
55 </param>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
56 <when value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
57 <when value="1">
21
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
58 <param name="ref_col" type="data_column" data_ref="input" numerical="false" label="Column with reference chromosome" help="Note: be sure this corresponds to the build recorded in the metadata."/>
d6b961721037 Miller Lab Devshed version 4c04e35b18f6
Richard Burhans <burhans@bx.psu.edu>
parents: 14
diff changeset
59 <param name="rpos_col" type="data_column" data_ref="input" numerical="true" label="Column with reference position" help="Note: either zero-based or one-based positions will work."/>
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
60 </when>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
61 </conditional>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
62 </inputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
63
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
64 <outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
65 <data name="output" format="interval">
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
66 <change_format>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
67 <when input="out_format" value="1" format="bigwigpos" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
68 </change_format>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
69 </data>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
70 </outputs>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
71
31
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 28
diff changeset
72 <requirements>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 28
diff changeset
73 <requirement type="package" version="0.1">gd_c_tools</requirement>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 28
diff changeset
74 </requirements>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 28
diff changeset
75
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
76 <tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
77 <test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
78 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
79 <param name="score_col" value="5" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
80 <param name="type" value="value" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
81 <param name="cutoff_val" value="700.0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
82 <param name="shuffles" value="10" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
83 <param name="out_format" value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
84 <param name="choice" value="0" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
85
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
86 <output name="output" file="test_out/find_intervals/find_intervals.interval" />
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
87 </test>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
88 </tests>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
89
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
90 <help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
91 **Dataset formats**
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
92
28
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
93 The input dataset is tabular_ (which includes gd_snp_ and gd_genotype_),
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
94 with required columns of chromosome, position, and score (in any column).
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
95 The output dataset is interval_. (`Dataset missing?`_)
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
96
28
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
97 .. _tabular: ./static/formatHelp.html#tab
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
98 .. _gd_snp: ./static/formatHelp.html#gd_snp
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
99 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
100 .. _interval: ./static/formatHelp.html#interval
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
101 .. _Dataset missing?: ./static/formatHelp.html
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
102
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
103 -----
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
104
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
105 **What it does**
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
106
28
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
107 The user selects a tabular dataset (such as the SNV formats gd_snp and
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
108 gd_genotype) and if the dataset is not in an SNV format, specifies the
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
109 columns containing chromosome, position, and scores (such as an FST-value
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
110 for the SNP). With SNV formats, the metadata tells which columns hold the
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
111 chromosome and position. Other inputs include a percentage or raw score
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
112 for the "score-shift" which should be greater than the average value
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
113 for the scores column. A higher value will give smaller intervals in
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
114 the output. If a percentage (e.g. 95%) is specified then that percentile
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
115 of the scores is used as the shift; percentile may not work well if many
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
116 rows or SNPs have the same score (in that case use a raw score).
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
117
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
118 The program subtracts the shift from every score, then finds genomic
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
119 intervals (i.e., consecutive runs of SNPs) whose total score cannot be
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
120 increased by adding or subtracting one or more adjusted scores at the
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
121 ends of the interval. Another input is the number of times the data
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
122 should be randomized (only intervals with score exceeding the maximum
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
123 for the randomized data are reported). If 100 shuffles are requested,
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
124 then any interval reported by the tool has a score with probability
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
125 less than 0.01 of being equaled or exceeded by chance, assuming that
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
126 the scores vary independently by position.
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
127
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
128 -----
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
129
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
130 **Example**
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
131
28
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
132 - Input (showing only the chromosome, position, and score columns)::
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
133
28
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
134 chr2 39 0.40
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
135 chr2 103 0.97
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
136 chr2 188 0.72
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
137 chr2 203 0.68
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
138 chr2 321 0.92
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
139 ...
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
140 chr2 1132 0.85
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
141 chr2 1321 0.34
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
142 ...
28
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
143
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
144 - Suppose the user-specified score-shift is 0.75. This value is subtracted from each score, giving::
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
145
28
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
146 chr2 39 -0.35
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
147 chr2 103 0.22
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
148 chr2 188 -0.03
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
149 chr2 203 -0.07
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
150 chr2 321 0.17
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
151 ...
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
152 chr2 1132 0.10
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
153 chr2 1321 -0.41
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
154 ...
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
155
28
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
156 - The output, not reporting individual positions, might be (depending on the values not shown above)::
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
157
28
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
158 chr2 103 1132 1.42
14
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
159 </help>
8ae67e9fb6ff Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]
miller-lab
parents:
diff changeset
160 </tool>
28
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
161
184d14e4270d Update to Miller Lab devshed revision 4ede22dd5500
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
162