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