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comparison tools/maf/maf_reverse_complement.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="MAF_Reverse_Complement_1" name="Reverse Complement" version="1.0.1">
2 <description>a MAF file</description>
3 <command interpreter="python">maf_reverse_complement.py $input1 $out_file1 $species</command>
4 <inputs>
5 <page>
6 <param format="maf" name="input1" label="Alignment File" type="data"/>
7 <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
8 <options>
9 <filter type="data_meta" ref="input1" key="species" />
10 </options>
11 </param>
12 </page>
13 </inputs>
14 <outputs>
15 <data format="maf" name="out_file1" metadata_source="input1"/>
16 </outputs>
17 <tests>
18 <test>
19 <param name="input1" value="3.maf" dbkey="hg17" format="maf"/>
20 <param name="species" value="hg17,panTro1,mm5,rn3,canFam1"/>
21 <output name="out_file1" file="maf_reverse_complement_out.dat"/>
22 </test>
23 </tests>
24 <help>
25 **What it does**
26
27 This tool takes a MAF file and creates a new MAF file, where each block has been reversed complemented.
28
29 **Example**
30
31 This MAF Block::
32
33 a score=8157.000000
34 s hg17.chr7 127471526 58 + 158628139 AATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG
35 s panTro1.chr6 129885407 58 + 161576975 AATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG
36 s mm5.chr6 28904928 54 + 149721531 AA----CGTTTCATTGATTGCTCATCATTTAAAAAAAGAAATTCCTCAGTGGAAGAGG
37
38 becomes::
39
40 a score=8157.000000
41 s hg17.chr7 31156555 58 - 158628139 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAATGAATAAACCACAAATT
42 s panTro1.chr6 31691510 58 - 161576975 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAACGAATAAACCACAAATT
43 s mm5.chr6 120816549 54 - 149721531 CCTCTTCCACTGAGGAATTTCTTTTTTTAAATGATGAGCAATCAATGAAACG----TT
44
45 ------
46
47 **Citation**
48
49 If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21775304&gt;`_
50
51
52 </help>
53 </tool>