Mercurial > repos > xuebing > sharplabtool

comparison tools/regVariation/getIndels_2way.xml @ 0:9071e359b9a3

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:9071e359b9a3
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
29 This tool estimates the number of indels for every alignment block of the MAF file.
30
31 -----
32
33 .. class:: warningmark
34
35 **Note**
36
37 Any 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>