Mercurial > repos > swebb > pycrac
comparison pyCRAC/pyAlignment2Tab.xml @ 0:19b20927172d draft
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| author | swebb |
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| date | Tue, 18 Jun 2013 09:11:00 -0400 |
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| -1:000000000000 | 0:19b20927172d |
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| 1 <tool id="pyAlignment2Tab" name="pyAlignment2Tab"> | |
| 2 <description>converter</description> | |
| 3 <requirements> | |
| 4 <requirement type="package">pyCRAC</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python">/usr/local/bin/pyAlignment2Tab.py -f $input --limit $limit -o $output --singlefile | |
| 7 </command> | |
| 8 <version_command>/usr/local/bin/pyAlignment2Tab.py --version</version_command> | |
| 9 <inputs> | |
| 10 <param name="input" type="data" format="fasta" label="pyReadAligner output file -f" help="Fasta file"/> | |
| 11 <param name="limit" type="integer" format="integer" value="90" size="4" label="Set the column width of alignment" help="Enter a value > 50"> | |
| 12 <validator type="in_range" min="50" message="Please enter a value greater than 50"/> | |
| 13 </param> | |
| 14 <param name="label" type="text" format="txt" size="30" value="pyAlignment2Tab" label="Enter output file label -o" /> | |
| 15 </inputs> | |
| 16 <outputs> | |
| 17 <data name="output" format="txt" label="${label.value}.tab"/> | |
| 18 </outputs> | |
| 19 <help> | |
| 20 | |
| 21 .. class:: infomark | |
| 22 | |
| 23 **pyAlignment2Tab** | |
| 24 | |
| 25 pyAlignment2Tab is part of the pyCRAC_ package. Converts pyReadAligner fasta output to a tabular alignment output. | |
| 26 | |
| 27 Example:: | |
| 28 | |
| 29 The tool expects a standard pyReadAligner fasta-formatted output file: | |
| 30 | |
| 31 >GeneX | |
| 32 ATGTCTCGTACTAACATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCACCACAGAGTGCTACTGCAAATAGCAGGAGCAGCAACAGCAGCAGCGAGAGTAGTAGTAACAAAAACAATATCAATGTCGGCGTCGGTGACGATAGCGGTAA | |
| 33 >257930-10 | |
| 34 ---TCTCGTACcAACATGGATACAAGACACGCACATTCTGCTT---------------------------------------------------------------------------------------------------------------- | |
| 35 >3664964-1 | |
| 36 ---TCTCGcACcAACATGGATACAAGACACGCACATTtTGCTT---------------------------------------------------------------------------------------------------------------- | |
| 37 >4033560-1 | |
| 38 ---TCTCGTACcAACATGGATACAAGACACGCACATTCTGtTT---------------------------------------------------------------------------------------------------------------- | |
| 39 >8571880-1 | |
| 40 ---TCTCGTACcAACATGGATACAAGACACGCAgATTCTGCTT---------------------------------------------------------------------------------------------------------------- | |
| 41 >9617396-1 | |
| 42 ---TCTCGTACcAACATGGATACAAGACACGCcCATTCTGCTT---------------------------------------------------------------------------------------------------------------- | |
| 43 >843368-5 | |
| 44 ------------AACAcGGATACAAGACACGCACATTCTG------------------------------------------------------------------------------------------------------------------- | |
| 45 >854553-5 | |
| 46 ------------AACATGGATACAAGACACGCAC--TCTG------------------------------------------------------------------------------------------------------------------- | |
| 47 >1522401-2 | |
| 48 --------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgA----------------------------------------------------------------------------------------------------- | |
| 49 >5981234-1 | |
| 50 --------------CATGGATACAAGACACGCACAcTCTGCTTTACTGGCAGCA----------------------------------------------------------------------------------------------------- | |
| 51 >997684-4 | |
| 52 --------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCA----------------------------------------------------------------------------------------------------- | |
| 53 >1046653-4 | |
| 54 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgAC---------------------------------------------------------------------------------------------------- | |
| 55 >1103730-4 | |
| 56 ---------------ATGGATACAAGACACGCACAcTCTG------------------------------------------------------------------------------------------------------------------- | |
| 57 >1603913-2 | |
| 58 ---------------ATGGATACAAGAaACGCACAcTCTG------------------------------------------------------------------------------------------------------------------- | |
| 59 >180349-12 | |
| 60 ---------------ATGGATACAAGACACGCACATTCcGCTTTACTG----------------------------------------------------------------------------------------------------------- | |
| 61 >1985106-1 | |
| 62 ---------------ATGGATACAAGACACGCACATTCgGCTTTACTGGCAGCcC---------------------------------------------------------------------------------------------------- | |
| 63 >1987775-1 | |
| 64 ---------------ATGGATACccGACACGCACATTCTGCTTTACTGcCAGCAC---------------------------------------------------------------------------------------------------- | |
| 65 >2258725-1 | |
| 66 ---------------ATGGATACAAGACACGCACATTCTGCTTTgCTGGCAGCAC---------------------------------------------------------------------------------------------------- | |
| 67 >2631987-1 | |
| 68 ---------------ATGGATACAAGACACGCACATTCTGCTTTACcGGCAGgAC---------------------------------------------------------------------------------------------------- | |
| 69 | |
| 70 This will be converted into: | |
| 71 | |
| 72 1 .........|.........|.........|.........|.........|.........|.........|.........|.........| 90 | |
| 73 >GeneX ATGTCTCGTACTAACATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCACCACAGAGTGCTACTGCAAATAGCAGGAGCAGCAAC | |
| 74 >257930-10 ---TCTCGTACcAACATGGATACAAGACACGCACATTCTGCTT----------------------------------------------- | |
| 75 >3664964-1 ---TCTCGcACcAACATGGATACAAGACACGCACATTtTGCTT----------------------------------------------- | |
| 76 >4033560-1 ---TCTCGTACcAACATGGATACAAGACACGCACATTCTGtTT----------------------------------------------- | |
| 77 >8571880-1 ---TCTCGTACcAACATGGATACAAGACACGCAgATTCTGCTT----------------------------------------------- | |
| 78 >9617396-1 ---TCTCGTACcAACATGGATACAAGACACGCcCATTCTGCTT----------------------------------------------- | |
| 79 >843368-5 ------------AACAcGGATACAAGACACGCACATTCTG-------------------------------------------------- | |
| 80 >854553-5 ------------AACATGGATACAAGACACGCAC--TCTG-------------------------------------------------- | |
| 81 >1522401-2 --------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgA------------------------------------ | |
| 82 >5981234-1 --------------CATGGATACAAGACACGCACAcTCTGCTTTACTGGCAGCA------------------------------------ | |
| 83 >997684-4 --------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCA------------------------------------ | |
| 84 >1046653-4 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgAC----------------------------------- | |
| 85 >1103730-4 ---------------ATGGATACAAGACACGCACAcTCTG-------------------------------------------------- | |
| 86 >1603913-2 ---------------ATGGATACAAGAaACGCACAcTCTG-------------------------------------------------- | |
| 87 >180349-12 ---------------ATGGATACAAGACACGCACATTCcGCTTTACTG------------------------------------------ | |
| 88 >1985106-1 ---------------ATGGATACAAGACACGCACATTCgGCTTTACTGGCAGCcC----------------------------------- | |
| 89 >1987775-1 ---------------ATGGATACccGACACGCACATTCTGCTTTACTGcCAGCAC----------------------------------- | |
| 90 >2258725-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTgCTGGCAGCAC----------------------------------- | |
| 91 >2631987-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACcGGCAGgAC----------------------------------- | |
| 92 >337206-9 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCAC----------------------------------- | |
| 93 >4616761-1 ---------------ATGGATAgAAGACACGCACATTCTGCTTTACTGGtAGCAC----------------------------------- | |
| 94 >4756312-1 ---------------ATGGATACAAcACACGCACAcTCTG-------------------------------------------------- | |
| 95 >4763682-1 ---------------ATGGATACAAGACACGCACATTCcGCTTTcCTG------------------------------------------ | |
| 96 >5971268-1 ---------------ATGGATACAAGACACGCACATTCcGCTcTACTc------------------------------------------ | |
| 97 >6644790-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTcGCAGCAC----------------------------------- | |
| 98 >7112423-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGtCAGCAC----------------------------------- | |
| 99 >7559990-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCcGgAC----------------------------------- | |
| 100 >8007281-1 ---------------ATGGATAtAAGACACGCACAcTCTG-------------------------------------------------- | |
| 101 >9150255-1 ---------------ATGGATACAcGACACGCACATTCcGCTTTcCTG------------------------------------------ | |
| 102 >9180814-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgcC----------------------------------- | |
| 103 >963117-4 ---------------ATGGATACAAGACACGCACATTCTGCTTTACcGGCAGCAC----------------------------------- | |
| 104 >9672073-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCcC----------------------------------- | |
| 105 >971218-4 ---------------ATGGATACAAGACACGCACATcCTGCTTTACTGG-AGCACC---------------------------------- | |
| 106 >10040274-1 -------------------ATACAAGACACGCACATTCTGCTTTACTGGCAGgACCACA------------------------------- | |
| 107 >1063072-4 -------------------ATACAAGACACGCACATTCTGCTTcACTGGCAGCACCACA------------------------------- | |
| 108 >1430188-2 -------------------ATACAAGACACGCACATTCTGCTTTACTGGCAGCACCACA------------------------------- | |
| 109 >5196741-1 -------------------ATACAAGACACGCACATTCTGCTTcACTGGCcGCACCACA------------------------------- | |
| 110 >6017337-1 -------------------ATACAAGACACGCACATTCTGCTTcACTGtCAGaACCcCA------------------------------- | |
| 111 >7159053-1 -------------------ATACAAGACACGCACATTCTGCTTTACTGGCAGCACCcaA------------------------------- | |
| 112 >7528336-1 -------------------ATACAAGACACGCACATTCTGCTTcACTGGCAGCAaCACA------------------------------- | |
| 113 >735584-6 --------------------------------------------------------ACAGAGTGCTACTGCAAAcAGCAGGAGCAGCAAC | |
| 114 >8551047-1 --------------------------------------------------------ACAGAGTGCTAtTGCAAAcAGCAGGAGtAGtAAC | |
| 115 >3000121-1 ------------------------------------------------------------AGTcCTACcGCAAATAGCAGcAGCAGCAAC | |
| 116 >928481-5 ------------------------------------------------------------AGTGCTACcGCAAATAGCAGGAGCAGCAAC | |
| 117 >126987-15 ----------------------------------------------------------------------CAAATAGCAGGAGCAGCAAC | |
| 118 >3122797-1 ----------------------------------------------------------------------CAAATAGCAGGcGCAGCAAC | |
| 119 >6684686-1 ----------------------------------------------------------------------CAAATAGCAGGAGCAGCAAC | |
| 120 | |
| 121 Note that the column width here was set to 90 characters | |
| 122 | |
| 123 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html | |
| 124 | |
| 125 ------ | |
| 126 | |
| 127 **Parameter list** | |
| 128 | |
| 129 Options:: | |
| 130 | |
| 131 -f data.fasta | |
| 132 Type the path to the fasta file that you want to use. | |
| 133 --limit=90 | |
| 134 Allows the user to set the column width of the alignment. Default=90 characters | |
| 135 -o output.fasta | |
| 136 Provide the name of your output file | |
| 137 | |
| 138 </help> | |
| 139 </tool> |