Mercurial > repos > galaxyp > nbic_fasta
comparison GenerateDegenerateFasta.xml @ 0:163892325845 draft default tip
Initial commit.
| author | galaxyp |
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| date | Fri, 10 May 2013 17:15:08 -0400 |
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| -1:000000000000 | 0:163892325845 |
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| 1 <!-- | |
| 2 # ===================================================== | |
| 3 # $Id: GenerateDegenerateFasta.xml 90 2011-01-19 13:20:31Z pieter.neerincx@gmail.com $ | |
| 4 # $URL: https://trac.nbic.nl/svn/galaxytools/trunk/tools/general/FastaTools/GenerateDegenerateFasta.xml $ | |
| 5 # $LastChangedDate: 2011-01-19 07:20:31 -0600 (Wed, 19 Jan 2011) $ | |
| 6 # $LastChangedRevision: 90 $ | |
| 7 # $LastChangedBy: pieter.neerincx@gmail.com $ | |
| 8 # ===================================================== | |
| 9 --> | |
| 10 <tool id="GenerateDegenerateFasta1" name="GenerateDegenerateFasta" version="2.1"> | |
| 11 <description>Creates a FASTA file with all possible sequences for degenerate sequences.</description> | |
| 12 <command interpreter="perl"> | |
| 13 #if $sequence_features.acid_type=="aa" #GenerateDegenerateFasta.pl -i $input -p $pcol -s $scol -t aa -o $output -x $sequence_features.xexpansion -l WARN | |
| 14 #elif $sequence_features.acid_type=="dna" #GenerateDegenerateFasta.pl -i $input -p $pcol -s $scol -t dna -o $output -l WARN | |
| 15 #elif $sequence_features.acid_type=="rna" #GenerateDegenerateFasta.pl -i $input -p $pcol -s $scol -t rna -o $output -l WARN | |
| 16 #end if | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <param format="tabular" name="input" type="data" label="Degenerate sequences" | |
| 20 help="(in tab delimited format)"/> | |
| 21 <param name="pcol" type="data_column" value="1" data_ref="input" label="Prefix column" | |
| 22 help="Prefixes will be used as the first part of unique identifiers for the generated sequences."/> | |
| 23 <param name="scol" type="data_column" value="2" data_ref="input" label="Sequence column"/> | |
| 24 <conditional name='sequence_features'> | |
| 25 <param name="acid_type" type="select" accept_default="true" mmultiple="false" label="The degenerate sequences represent"> | |
| 26 <label>The degenerate sequences represent</label> | |
| 27 <option value="aa">Proteins</option> | |
| 28 <option value="dna">DNA</option> | |
| 29 <option value="rna">RNA</option> | |
| 30 </param> | |
| 31 <when value="aa"> | |
| 32 <param name="xexpansion" type="select" accept_default="true" mmultiple="false" label="The degenerate amino acid X represents"> | |
| 33 <label>The degenerate amino acid X represents</label> | |
| 34 <option value="20">The 20 most common amino acids</option> | |
| 35 <option value="22">All 22 amino acids</option> | |
| 36 </param> | |
| 37 </when> | |
| 38 <when value="dna"> | |
| 39 </when> | |
| 40 <when value="rna"> | |
| 41 </when> | |
| 42 </conditional> | |
| 43 </inputs> | |
| 44 <outputs> | |
| 45 <data format="fasta" name="output" label="FASTA sequences for ${input.name}"/> | |
| 46 </outputs> | |
| 47 <!-- | |
| 48 <tests> | |
| 49 <test> | |
| 50 <param name="input" value="GenerateDegenerateFasta_example_input.txt"/> | |
| 51 <output name="output" file="GenerateDegenerateFasta_example_output.fasta" ftype="fasta"/> | |
| 52 </test> | |
| 53 </tests> | |
| 54 --> | |
| 55 <help> | |
| 56 | |
| 57 .. class:: infomark | |
| 58 | |
| 59 **What it does** | |
| 60 | |
| 61 This tool creates a multi-sequence FASTA file with all possible sequences based on degenerate input sequences. | |
| 62 The input must be a tab delimited file containing at least 2 columns. | |
| 63 One with the degenerate sequences and the other with a prefix that will be used to give each of generated sequences a unique identifier. | |
| 64 In addition to the prefix, the generated identifiers will contain an underscore followed by an incremented number. | |
| 65 | |
| 66 =================================================== | |
| 67 *Degenerate (wild card) amino acids* | |
| 68 =================================================== | |
| 69 | |
| 70 ===================== =========================================== ==================================================================== | |
| 71 Amino Acid Expands to Comment | |
| 72 ===================== =========================================== ==================================================================== | |
| 73 B D,N | |
| 74 J I,L | |
| 75 X A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y The 20 most common amino acids (default) or | |
| 76 X A,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S,T,U,V,W,Y All 22 amino acids including the rare Selenocysteine and Pyrrolysine | |
| 77 Z E,Q | |
| 78 ===================== =========================================== ==================================================================== | |
| 79 | |
| 80 =================================================== | |
| 81 *Degenerate (wild card) deoxyribonucleic acids* | |
| 82 =================================================== | |
| 83 | |
| 84 ===================== ================================ =============================================================================== | |
| 85 Deoxyribonucleic Acid Expands to Comment | |
| 86 ===================== ================================ =============================================================================== | |
| 87 B C,G,T Not A; B follows A alphabetically | |
| 88 D A,G,T Not C; D follows C alphabetically | |
| 89 H A,C,T Not G; H follows G alphabetically | |
| 90 K G,T Keto | |
| 91 M A,C aMino | |
| 92 N A,C,G,T aNy | |
| 93 R A,G puRine | |
| 94 S C,G Strong interaction (3 H-bonds) | |
| 95 V A,C,G Not T (and not U); V follows U alphabetically | |
| 96 W A,T Weak interaction (2 H-bonds) | |
| 97 Y C,T pYrimidine | |
| 98 ===================== ================================ =============================================================================== | |
| 99 | |
| 100 =================================================== | |
| 101 *Degenerate (wild card) ribonucleic acids* | |
| 102 =================================================== | |
| 103 | |
| 104 ===================== ================================ =============================================================================== | |
| 105 Ribonucleic Acid Expands to Comment | |
| 106 ===================== ================================ =============================================================================== | |
| 107 B C,G,U Not A; B follows A alphabetically | |
| 108 D A,G,U Not C; D follows C alphabetically | |
| 109 H A,C,U Not G; H follows G alphabetically | |
| 110 K G,U Keto | |
| 111 M A,C aMino | |
| 112 N A,C,G,U aNy | |
| 113 R A,G puRine | |
| 114 S C,G Strong interaction (3 H-bonds) | |
| 115 V A,C,G Not U; V follows U alphabetically | |
| 116 W A,U Weak interaction (2 H-bonds) | |
| 117 Y C,U pYrimidine | |
| 118 ===================== ================================ =============================================================================== | |
| 119 | |
| 120 ----- | |
| 121 | |
| 122 **Example** | |
| 123 | |
| 124 If the degenerate input contains these two peptides:: | |
| 125 | |
| 126 Seq1 AXY | |
| 127 Seq2 SJT | |
| 128 | |
| 129 The generated FASTA sequences will be this:: | |
| 130 | |
| 131 >Seq1_1 | |
| 132 AAY | |
| 133 >Seq1_2 | |
| 134 ACY | |
| 135 >Seq1_3 | |
| 136 ADY | |
| 137 >Seq1_4 | |
| 138 AEY | |
| 139 >Seq1_5 | |
| 140 AFY | |
| 141 >Seq1_6 | |
| 142 AGY | |
| 143 >Seq1_7 | |
| 144 AHY | |
| 145 >Seq1_8 | |
| 146 AIY | |
| 147 >Seq1_9 | |
| 148 AKY | |
| 149 >Seq1_10 | |
| 150 ALY | |
| 151 >Seq1_11 | |
| 152 AMY | |
| 153 >Seq1_12 | |
| 154 ANY | |
| 155 >Seq1_13 | |
| 156 APY | |
| 157 >Seq1_14 | |
| 158 AQY | |
| 159 >Seq1_15 | |
| 160 ARY | |
| 161 >Seq1_16 | |
| 162 ASY | |
| 163 >Seq1_17 | |
| 164 ATY | |
| 165 >Seq1_18 | |
| 166 AVY | |
| 167 >Seq1_19 | |
| 168 AWY | |
| 169 >Seq1_20 | |
| 170 AYY | |
| 171 >Seq2_1 | |
| 172 SIT | |
| 173 >Seq2_2 | |
| 174 SLT | |
| 175 | |
| 176 </help> | |
| 177 </tool> |