[2] | 1 | <tool id="MAF_Thread_For_Species1" name="Join MAF blocks"> |
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| 2 | <description>by Species</description> |
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| 3 | <command interpreter="python">maf_thread_for_species.py $input1 $out_file1 $species</command> |
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| 4 | <inputs> |
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| 5 | <param format="maf" name="input1" type="data" label="MAF file"/> |
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| 6 | <param name="species" type="select" label="Species to keep" display="checkboxes" multiple="true"> |
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| 7 | <options> |
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| 8 | <filter type="data_meta" ref="input1" key="species" /> |
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| 9 | </options> |
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| 10 | </param> |
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| 11 | </inputs> |
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| 12 | <outputs> |
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| 13 | <data format="maf" name="out_file1" metadata_source="input1"/> |
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| 14 | </outputs> |
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| 15 | <tests> |
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| 16 | <test> |
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| 17 | <param name="input1" value="3.maf" format="maf"/> |
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| 18 | <param name="species" value="hg17,panTro1"/> |
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| 19 | <output name="out_file1" file="maf_thread_for_species.dat"/> |
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| 20 | </test> |
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| 21 | </tests> |
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| 22 | <help> |
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| 23 | |
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| 24 | **What it does** |
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| 25 | |
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| 26 | This tool allows the user to merge MAF blocks which are adjoining in each specified species from a MAF file. Columns which contain only gaps are removed. Species which are not desired are removed from the output. |
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| 27 | |
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| 28 | **Example** |
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| 29 | |
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| 30 | Specifying the desired species as hg17 and panTro1 with this MAF file:: |
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| 31 | |
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| 32 | ##maf version=1 |
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| 33 | a score=60426.000000 |
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| 34 | s hg17.chr7 127471195 331 + 158628139 gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAA |
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| 35 | s panTro1.chr6 129885076 331 + 161576975 gtttgccatcttttgctgctcttgggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTGAAACTTCCC-------------------------------AAATACT-GCCACTGATGTCCTG-----ATGGAGGTA-------TGAA-------------------AACATCCACTAA |
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| 36 | s mm5.chr6 28904571 357 + 149721531 CTCCACTCTCGTTTGCTGTT----------------CTGTCACCATGGAAACAAA-CGAGGGTGGTCCAGTTACTATCTTGACTGCAGCTGGCAGTCAGTT-GCCACT-----CAGGAATAAGGCTATGCCATT-GATCCACTGAACCGTGATCTGGAAACCTGGCTGTTGTTT-------CAAGCCTTGGGGCCAGTTTGCGGTGTTACTCATGA--CTCTAAGATCGTGTGCTTG----CTGCAGGAAGAGACAGCAAGGGGGTTACATTTAAAAAGCCCCCAGTTTAGCTATAGGCAGGCCAACAGGTGTAAAAATACTCACTAGTAATGGGCTGAACTCATGGAGGTAGCATTAGTGAGACACTGTAACTGTTTTTTTAAAAATCACTAA |
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| 37 | s rn3.chr4 56178191 282 + 187371129 CTTCACTCTCATTTGCTGTT----------------CTGTCACTATGGAGACAAACACAGGCTAGCCCAGTTACTATCTTGATCACAGCAGCT-GTCAGCTAGCTGCCACTCACAGGAATAAGGCCATACCATT-GATCCACTGAACCTTGATCTAGGAATTTGGC----------------------TGGGGCCAGTTTGCGGTGTCACTCATGA--CTCTAAGATTGTGTGTTTG----CTCCAGGAAGAGACGGCAAGAGGATTACCTTTAAAAGGTTC---------------------------------GGAGTCTAGCTGTAGACAGCCCA-----ATG--GGTA-------TAAC-------------------AATACTCACTAA |
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| 38 | |
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| 39 | a score=8157.000000 |
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| 40 | s hg17.chr7 127471526 58 + 158628139 AATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG |
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| 41 | s panTro1.chr6 129885407 58 + 161576975 AATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG |
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| 42 | s mm5.chr6 28904928 54 + 149721531 AA----CGTTTCATTGATTGCTCATCATTTAAAAAAAGAAATTCCTCAGTGGAAGAGG |
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| 43 | |
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| 44 | results in:: |
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| 45 | |
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| 46 | ##maf version=1 |
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| 47 | a score=0.0 |
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| 48 | s hg17.chr7 127471195 389 + 158628139 gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGGTATGAAAACATCCACTAAAATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG |
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| 49 | s panTro1.chr6 129885076 389 + 161576975 gtttgccatcttttgctgctcttgggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTGAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGGTATGAAAACATCCACTAAAATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG |
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| 50 | |
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| 51 | |
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| 52 | |
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| 53 | </help> |
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| 54 | </tool> |
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| 55 | |
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