Mercurial > repos > devteam > getindels_2way
annotate getIndels_2way.xml @ 1:f1dc6f5fce6e default tip
Corrected version string.
author | devteam <devteam@galaxyproject.org> |
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date | Thu, 10 Apr 2014 13:47:30 -0400 |
parents | 91655316fcf0 |
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f1dc6f5fce6e
Corrected version string.
devteam <devteam@galaxyproject.org>
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1 <tool id="getIndels_2way" name="Fetch Indels" version="1.0.0"> |
0 | 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> |