/tools/maf/maf_reverse_complement.xml

 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
27This tool takes a MAF file and creates a new MAF file, where each block has been reversed complemented.
28
29**Example**
30  
31This 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
38becomes::
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  </help>
45</tool>