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/tools/regVariation/getIndels_3way.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 53 lines | 40 code | 12 blank | 1 comment | 0 complexity | 41dac6d59e03ca1b6c6644f8ca03ee20 MD5 | raw file
 1<tool id="indels_3way" name="Fetch Indels"  version="1.0.3">
 2  <description> from 3-way alignments</description>
 3  <command interpreter="perl">
 4  	parseMAF_smallIndels.pl $input1 $out_file1 $outgroup
 5  </command>
 6  <inputs>
 7    <page>
 8    	<param format="maf" name="input1" type="data" label="Select data"/>
 9    	<param name="outgroup" type="select" label="Select outgroup species">
10          <options>
11            <filter type="data_meta" ref="input1" key="species" />
12          </options>  
13      	</param>
14    </page>
15  </inputs>
16  <outputs>
17    <data format="tabular" name="out_file1" metadata_source="input1"/>
18    <!--<data format="tabular" name="out_file2" metadata_source="input1"/>-->
19  </outputs>
20  <tests>
21    <test>
22      <param name="input1" value="3way.maf"/>
23      <param name="outgroup" value="canFam2"/>
24      <output name="out_file1" file="indels_3way.tabular"/>
25    </test>
26  </tests>
27 <help> 
28
29.. class:: infomark
30
31**What it does**
32
33This tool consists of the first module from the computational pipeline to identify indels as described in Kvikstad et al., 2007. Note that the generated output does not include subsequent filtering steps.
34
35Deletions in a particular species are identified as one or more consecutive gap columns within an alignment block, given that the orthologous positions in the other two species contain nucleotides of
36equal length. 
37Similarly, insertions in a particular species are identified as one or more consecutive nucleotide columns within an alignment block, given that the orthologous positions in the other two
38species contain gaps.
39
40*Kvikstad E. M. et al. (2007). A Macaques-Eye View of Human Insertions and Deletions: Differences in Mechanisms. PLoS Computational Biology 3(9):e176*
41
42-----
43
44.. class:: warningmark
45
46**Note**
47
48Any block/s not containing exactly 3 sequences will be omitted. 
49
50  </help>  
51
52
53</tool>