[2] | 1 | <tool id="MAF_Reverse_Complement_1" name="Reverse Complement" version="1.0.1">
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| 2 | <description>a MAF file</description>
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| 3 | <command interpreter="python">maf_reverse_complement.py $input1 $out_file1 $species</command>
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| 4 | <inputs>
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| 5 | <page>
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| 6 | <param format="maf" name="input1" label="Alignment File" type="data"/>
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| 7 | <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
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| 8 | <options>
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| 9 | <filter type="data_meta" ref="input1" key="species" />
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| 10 | </options>
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| 11 | </param>
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| 12 | </page>
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| 13 | </inputs>
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| 14 | <outputs>
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| 15 | <data format="maf" name="out_file1" metadata_source="input1"/>
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| 16 | </outputs>
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| 17 | <tests>
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| 18 | <test>
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| 19 | <param name="input1" value="3.maf" dbkey="hg17" format="maf"/>
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| 20 | <param name="species" value="hg17,panTro1,mm5,rn3,canFam1"/>
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| 21 | <output name="out_file1" file="maf_reverse_complement_out.dat"/>
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| 22 | </test>
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| 23 | </tests>
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| 24 | <help>
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| 25 | **What it does**
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| 26 |
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| 27 | This tool takes a MAF file and creates a new MAF file, where each block has been reversed complemented.
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| 28 |
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| 29 | **Example**
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| 30 |
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| 31 | This MAF Block::
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| 32 |
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| 33 | a score=8157.000000
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| 34 | s hg17.chr7 127471526 58 + 158628139 AATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG
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| 35 | s panTro1.chr6 129885407 58 + 161576975 AATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG
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| 36 | s mm5.chr6 28904928 54 + 149721531 AA----CGTTTCATTGATTGCTCATCATTTAAAAAAAGAAATTCCTCAGTGGAAGAGG
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| 37 |
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| 38 | becomes::
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| 39 |
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| 40 | a score=8157.000000
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| 41 | s hg17.chr7 31156555 58 - 158628139 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAATGAATAAACCACAAATT
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| 42 | s panTro1.chr6 31691510 58 - 161576975 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAACGAATAAACCACAAATT
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| 43 | s mm5.chr6 120816549 54 - 149721531 CCTCTTCCACTGAGGAATTTCTTTTTTTAAATGATGAGCAATCAATGAAACG----TT
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| 44 | </help>
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| 45 | </tool>
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