/tools/regVariation/getIndels_2way.xml

 1<tool id="getIndels_2way" name="Fetch Indels">
 2  <description> from pairwise alignments</description>
 3  <command interpreter="python">
 4  	getIndels.py $input1 $out_file1
 5  </command>
 6  <inputs>
 7    <page>
 8    	<param format="maf" name="input1" type="data" label="Select data"/>
 9    </page>
10  </inputs>
11  <outputs>
12    <data format="tabular" name="out_file1" metadata_source="input1"/>
13  </outputs>
14  <requirements>
15    <requirement type="python-module">numpy</requirement>
16  </requirements>
17  <tests>
18    <test>
19      <param name="input1" value="6.maf"/>
20      <output name="out_file1" file="6_indels.tabular"/>
21    </test>
22  </tests>
23 <help> 
24
25.. class:: infomark
26
27**What it does**
28
29This tool estimates the number of indels for every alignment block of the MAF file. 
30
31-----
32
33.. class:: warningmark
34
35**Note**
36
37Any block/s not containing exactly 2 species will be omitted. 
38
39-----
40
41**Example**
42
43- For the following alignment block::
44
45   a score=7233.0
46   s hg18.chr1     100 35 + 247249719 AT--GACTGAGGACTTAGTTTAAGATGTTCCTACT
47   s rheMac2.chr11 200 31 + 134511895 ATAAG-CGGACGACTTAGTTTAAGATGTTCC---- 
48
49- running this tool will return::
50
51   #Block   Source	      Seq1_Start	Seq1_End  Seq2_Start	Seq2_End	Indel_length
52   1	   hg18.chr1            101	         102	     202	     204	      2
53   1	   rheMac2.chr11	103	         104	     204	     205	      1
54   1	   rheMac2.chr11	129	         133	     229	     230	      4
55   
56</help>  
57
58
59</tool>