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54 lines
2.1 KiB
XML
54 lines
2.1 KiB
XML
<tool id="MAF_Reverse_Complement_1" name="Reverse Complement" version="1.0.1">
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<description>a MAF file</description>
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<command interpreter="python">maf_reverse_complement.py $input1 $out_file1 $species</command>
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<inputs>
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<page>
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<param format="maf" name="input1" label="Alignment File" type="data"/>
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<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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<options>
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<filter type="data_meta" ref="input1" key="species" />
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</options>
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</param>
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</page>
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</inputs>
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<outputs>
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<data format="maf" name="out_file1" metadata_source="input1"/>
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</outputs>
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<tests>
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<test>
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<param name="input1" value="3.maf" dbkey="hg17" format="maf"/>
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<param name="species" value="hg17,panTro1,mm5,rn3,canFam1"/>
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<output name="out_file1" file="maf_reverse_complement_out.dat"/>
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</test>
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</tests>
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<help>
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**What it does**
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This tool takes a MAF file and creates a new MAF file, where each block has been reversed complemented.
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**Example**
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This MAF Block::
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a score=8157.000000
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s hg17.chr7 127471526 58 + 158628139 AATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG
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s panTro1.chr6 129885407 58 + 161576975 AATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG
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s mm5.chr6 28904928 54 + 149721531 AA----CGTTTCATTGATTGCTCATCATTTAAAAAAAGAAATTCCTCAGTGGAAGAGG
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becomes::
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a score=8157.000000
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s hg17.chr7 31156555 58 - 158628139 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAATGAATAAACCACAAATT
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s panTro1.chr6 31691510 58 - 161576975 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAACGAATAAACCACAAATT
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s mm5.chr6 120816549 54 - 149721531 CCTCTTCCACTGAGGAATTTCTTTTTTTAAATGATGAGCAATCAATGAAACG----TT
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------
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**Citation**
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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. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_
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</help>
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</tool>
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