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comparison getIndels_2way.xml @ 0:d6d2391a1cbb

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Imported from capsule None
author devteam
date Tue, 01 Apr 2014 09:12:57 -0400
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children 51ee76168a2d
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1 <tool id="getIndels_2way" name="Fetch Indels" version="0.0.1">
2 <description> from pairwise alignments</description>
3 <requirements>
4 <requirement type="package" version="1.7.1">numpy</requirement>
5 <requirement type="package" version="0.7.1">bx-python</requirement>
6 </requirements>
7 <command interpreter="python">
8 getIndels.py $input1 $out_file1
9 </command>
10 <inputs>
11 <page>
12 <param format="maf" name="input1" type="data" label="Select data"/>
13 </page>
14 </inputs>
15 <outputs>
16 <data format="tabular" name="out_file1" metadata_source="input1"/>
17 </outputs>
18 <requirements>
19 <requirement type="python-module">numpy</requirement>
20 </requirements>
21 <tests>
22 <test>
23 <param name="input1" value="6.maf"/>
24 <output name="out_file1" file="6_indels.tabular"/>
25 </test>
26 </tests>
27 <help>
28
29 .. class:: infomark
30
31 **What it does**
32
33 This tool estimates the number of indels for every alignment block of the MAF file.
34
35 -----
36
37 .. class:: warningmark
38
39 **Note**
40
41 Any block/s not containing exactly 2 species will be omitted.
42
43 -----
44
45 **Example**
46
47 - For the following alignment block::
48
49 a score=7233.0
50 s hg18.chr1 100 35 + 247249719 AT--GACTGAGGACTTAGTTTAAGATGTTCCTACT
51 s rheMac2.chr11 200 31 + 134511895 ATAAG-CGGACGACTTAGTTTAAGATGTTCC----
52
53 - running this tool will return::
54
55 #Block Source Seq1_Start Seq1_End Seq2_Start Seq2_End Indel_length
56 1 hg18.chr1 101 102 202 204 2
57 1 rheMac2.chr11 103 104 204 205 1
58 1 rheMac2.chr11 129 133 229 230 4
59
60 </help>
61
62
63 </tool>