/tools/maf/maf_reverse_complement.xml
XML | 45 lines | 39 code | 6 blank | 0 comment | 0 complexity | ba90df39f379a120d42b9b0f76a6861d MD5 | raw file
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>