comparison tools/regVariation/getIndelRates_3way.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 <tool id="indelRates_3way" name="Estimate Indel Rates" version="1.0.0">
2 <description> for 3-way alignments</description>
3 <command interpreter="python">
4 getIndelRates_3way.py $input1 $out_file1
5 #if $region.type == "align"
6 "None"
7 #else
8 $region.input2 $input2.dbkey $input2.metadata.chromCol,$input2.metadata.startCol,$input2.metadata.endCol,$input2.metadata.strandCol
9 #end if
10 </command>
11 <inputs>
12 <page>
13 <param format="tabular" name="input1" type="data" label="Select dataset containing Indels"/>
14
15 <conditional name="region">
16 <param name="type" type="select" label="Estimate rates corresponding to" multiple="false">
17 <option value="win" selected="True">Intervals in your history</option>
18 <option value="align">Alignment block</option>
19 </param>
20 <when value="win">
21 <param format="interval" name="input2" type="data" label="Choose intervals">
22 <validator type="unspecified_build" />
23 </param>
24 </when>
25 <when value="align" />
26 </conditional>
27
28 </page>
29 </inputs>
30 <outputs>
31 <data format="tabular" name="out_file1" metadata_source="input1"/>
32 </outputs>
33
34 <tests>
35 <test>
36 <param name="input1" value="indels_3way.tabular"/>
37 <param name="type" value="align"/>
38 <output name="out_file1" file="indelrates_3way.tabular"/>
39 </test>
40 </tests>
41
42 <help>
43
44 .. class:: infomark
45
46 **What it does**
47
48 This tool estimates the insertion and deletion rates for alignments in a window of specified size. Rates are computed over the total adjusted lengths (adjusted by disregarding masked bases) of all the alignments blocks from the indel file that fall within that window.
49
50 -----
51
52 .. class:: warningmark
53
54 **Note**
55
56 This tool only works on the output of the 'Estimate Indel Rates for 3-way alignments' tool.
57
58 </help>
59
60
61 </tool>