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1 <!--
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2 # =====================================================
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3 # $Id: ConvertFastaHeaders.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/ConvertFastaHeaders.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="ConvertFastaHeaders1" name="ConvertFastaHeaders" version="2.0">
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11 <description>Converts sequence headers of FASTA files</description>
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12 <command interpreter="perl">
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13 #if $mode.action == "add" #ConvertFastaHeaders.pl -i $input -o $output -p $mode.pos.position -a $mode.action -f "$mode.pos.xfixes" -l ERROR
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14 #elif $mode.action == "strip" #ConvertFastaHeaders.pl -i $input -o $output -p $mode.pos.position -a $mode.action -f "$mode.pos.xfixes" -l ERROR
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15 #elif $mode.action == "replace" #ConvertFastaHeaders.pl -i $input -o $output -p $mode.pos.position -a $mode.action -f "$mode.pos.xfixes" -n $mode.pos.newfix -l ERROR
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16 #elif $mode.action == "delete" #ConvertFastaHeaders.pl -i $input -o $output -p $mode.position -a $mode.action -l ERROR
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17 #elif $mode.action == "shuffle" #ConvertFastaHeaders.pl -i $input -o $output -p $mode.position -a $mode.action -l ERROR
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18 #end if
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19 </command>
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20 <inputs>
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21 <param format="fasta" name="input" type="data" label="FASTA sequences"/>
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22 <conditional name ="mode">
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23 <param name="action" type="select">
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24 <label>Action to perform on sequence identifiers</label>
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25 <option value="add">Add Labels</option>
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26 <option value="strip">Remove Labels</option>
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27 <option value="replace">Replace Labels</option>
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28 <option value="delete">Delete</option>
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29 <option value="shuffle">Shuffle order</option>
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30 </param>
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31 <when value="add">
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32 <conditional name="pos">
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33 <param name="position" type="select" accept_default="true">
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34 <label> Label position </label>
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35 <option value="prefix">Prepend Prefixes</option>
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36 <option value="suffix">Append Suffixes</option>
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37 </param>
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38 <when value="prefix">
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39 <param name="xfixes" type="text" label="Space separated list of prefixes, which will be added"/>
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40 </when>
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41 <when value="suffix">
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42 <param name="xfixes" type="text" label="Space separated list of suffixes, which will be added"/>
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43 </when>
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44 </conditional>
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45 </when>
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46 <when value="strip">
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47 <conditional name="pos">
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48 <param name="position" type="select" accept_default="true">
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49 <label> Label position </label>
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50 <option value="prefix">Strip Prefixes</option>
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51 <option value="suffix">Strip Suffixes</option>
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52 </param>
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53 <when value="prefix">
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54 <param name="xfixes" type="text" label="Space separated list of prefixes, which will be removed"/>
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55 </when>
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56 <when value="suffix">
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57 <param name="xfixes" type="text" label="Space separated list of suffixes, which will be removed"/>
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58 </when>
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59 </conditional>
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60 </when>
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61 <when value="replace">
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62 <conditional name="pos">
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63 <param name="position" type="select" accept_default="true">
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64 <label> Label position </label>
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65 <option value="prefix">Replace prefixes with another prefix</option>
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66 <option value="suffix">Replace suffixes with another suffix</option>
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67 <option value="pre2suf">Replace prefixes with a suffix</option>
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68 <option value="suf2pre">Replace suffixes with a prefix</option>
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69 </param>
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70 <when value="prefix">
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71 <param name="xfixes" type="text" label="Space separated list of prefixes, which will be replaced"/>
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72 <param name="newfix" type="text" label="New prefix to replace the current prefixes"/>
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73 </when>
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74 <when value="suffix">
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75 <param name="xfixes" type="text" label="Space separated list of suffixes, which will be replaced"/>
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76 <param name="newfix" type="text" label="New suffix to replace the current suffixes"/>
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77 </when>
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78 <when value="pre2suf">
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79 <param name="xfixes" type="text" label="Space separated list of prefixes, which will be replaced"/>
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80 <param name="newfix" type="text" label="New suffix to replace the current prefixes"/>
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81 </when>
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82 <when value="suf2pre">
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83 <param name="xfixes" type="text" label="Space separated list of suffixes, which will be replaced"/>
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84 <param name="newfix" type="text" label="New prefix to replace the current suffixes"/>
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85 </when>
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86 </conditional>
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87 </when>
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88 <when value="delete">
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89 <param name="position" type="text" size="10" value="" label="Ranks of IDs to delete"
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90 help="Comma separated list of numbers. For example 1,3 will delete the first and third ID from the FASTA headers."/>
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91 </when>
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92 <when value="shuffle">
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93 <param name="position" type="text" size="10" value="" label="New order for the IDs"
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94 help="Comma separated list of numbers. For example 1,3,2 will shuffle the order from 1,2,3 to 1,3,2."/>
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95 </when>
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96 </conditional>
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97 </inputs>
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98 <outputs>
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99 <data format="fasta" name="output" label="${input.name} with converted FASTA headers"/>
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100 </outputs>
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101 <!--
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102 <tests>
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103 <test> -a add -f "UniProt-Acc: UniProt-ID:"
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104 <param name="input" value="ConvertFastaHeaders_example_input_Add.fasta"/>
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105 <output name="output" file="ConvertFastaHeaders_example_output_Add.fasta"/>
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106 </test>
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107 <test> -a strip -p prefix -f 'SP:'
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108 <param name="input" value="ExtractPeptideSequenceContext_example_DB.fasta"/>
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109 <output name="output" file="ConvertFastaHeaders_example_output_Strip.fasta"/>
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110 </test>
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111 <test> -a replace -p pre2suf -f 'SP:' -n '_CON'
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112 <param name="input" value="ExtractPeptideSequenceContext_example_DB.fasta"/>
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113 <output name="output" file="ConvertFastaHeaders_example_output_Replace.fasta"/>
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114 </test>
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115 <test> -a delete -p '1 3'
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116 <param name="input" value="ExtractPeptideSequenceContext_example_DB.fasta"/>
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117 <output name="output" file="ConvertFastaHeaders_example_output_Delete.fasta"/>
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118 </test>
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119 <test> -a shuffle -p '2 3 1'
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120 <param name="input" value="ExtractPeptideSequenceContext_example_DB.fasta"/>
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121 <output name="output" file="ConvertFastaHeaders_example_output_Shuffle.fasta"/>
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122 </test>
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123 </tests>
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124 -->
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125 <help>
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126
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127 .. class:: infomark
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128
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129 **What it does**
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130
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131 This tool converts the sequence headers (the description line starting with >) for a set of FASTA sequences. \
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132 Currently supported conversions:
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133
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134 - Append prefixes like for example database namespace to identifiers / accession numbers.
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135 - Append suffixes to identifiers / accession numbers.
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136 - Remove prefixes like for example database namespace from identifiers / accession numbers.
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137 - Remove suffixes from identifiers / accession numbers.
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138 - Replace prefixes with a suffix or vice versa.
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139
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140 -----
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141
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142 **Examples**
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143
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144 ========================================================
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145 *Appending database namespace prefixes*
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146 ========================================================
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147
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148 Supply a space separated list of prefixes to add to pipe separated identifiers. \
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149 The prefixes must contain both the database namespace you want to add and the character used to separate the namespace from the identifier. \
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150 The order of the namespaces is important in this case! \
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151 For example with action *Add Labels*, label position *Prepend Prefixes* and prefixes *UniProtAcc: UniProtID:*, this header::
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152
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153 >P32234|128UP_DROME GTP-binding protein 128up - Drosophila melanogaster (Fruit fly)
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154
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155 will be converted into::
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156
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157 >UniProtAcc:P32234|UniProtID:128UP_DROME GTP-binding protein 128up - Drosophila melanogaster (Fruit fly)
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158
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159 ========================================================
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160 *Removing database namespace prefixes*
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161 ========================================================
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162
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163 Supply a space separated list of namespaces to remove from pipe separated identifiers. \
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164 The prefixes must contain both the database namespace you want to remove and the character used to separate the namespace from the identifier. \
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165 The order of the namespaces is not relevant in this case. \
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166 For example with action *Remove Labels*, label position *Strip Prefixes* and \
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167 with prefixes *UniProtAcc: UniProtID:* or with prefixes *UniProtID: UniProtAcc:*, this header::
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168
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169 >UniProtAcc:P32234|UniProtID:128UP_DROME GTP-binding protein 128up - Drosophila melanogaster (Fruit fly)
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170
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171 will be converted into::
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172
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173 >P32234|128UP_DROME GTP-binding protein 128up - Drosophila melanogaster (Fruit fly)
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174
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175 ========================================================
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176 *Replacing a prefix with a suffix*
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177 ========================================================
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178
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179 Supply the prefix to remove from pipe separated identifiers and a new suffix. \
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180 The order of the prefixes is not relevant in this case. \
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181 Optionally you can specify more than one prefix to remove by separating them with spaces. \
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182 You can specify only one new suffix though, so in case you specified more than one prefix they will all be replaced with the same new suffix. \
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183 In the following example we'll replace a *REV_* prefix to indicate a reversed sequence with a *_REV* suffix. \
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184 With action *Replace Labels*, label position *Replace prefixes with a suffix*, prefix *REV_* and new suffix *_REV*, this header::
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185
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186 >REV_P32234|128UP_DROME GTP-binding protein 128up - Drosophila melanogaster (Fruit fly)
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187
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188 will be converted into::
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189
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190 >P32234_REV|128UP_DROME GTP-binding protein 128up - Drosophila melanogaster (Fruit fly)
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191
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192 ========================================================
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193 *Other \*fix replacements*
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194 ========================================================
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195
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196 You can also replace a prefix with a new prefix, a suffix with a new suffix or a suffix with a new prefix. \
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197 These replacements are all similar to the example above. \
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198 Hence you can specify multiple \*-fixes to be replaced and only one new \*-fix to replace the existing ones.
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199
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200 ========================================================
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201 *Deleting sequence identifiers*
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202 ========================================================
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203
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204 Supply a comma separated list of numbers for the ranks of the identifiers / accession numbers you want to remove. \
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205 Multiple identifiers must be separated with a pipe symbol. \
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206 For example with action *Delete*, and Ranks of IDs to delete set to *1,3*, this header::
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207
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208 >UniProtID:128UP_DROME|UniProtAcc:P32234|EMBL:AY069810 GTP-binding protein 128up - Drosophila melanogaster (Fruit fly)
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209
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210 will be converted into::
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211
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212 >UniProtAcc:P32234 GTP-binding protein 128up - Drosophila melanogaster (Fruit fly)
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213
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214 ========================================================
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215 *Changing the order of sequence identifiers*
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216 ========================================================
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217
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218 Supply a comma separated list of numbers for the new order of all the identifiers / accession numbers in a header. \
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219 Multiple identifiers must be separated with a pipe symbol. \
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220 Hence if your headers contain 4 pipe separated IDs and you only want to swap the order of the first and the second, \
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221 you will still need to specify the new (unchanged) order for number 3 and 4 too.
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222
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223 For example with action *Shuffle*, and New order for the IDs set to *2,1,3*, this header::
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224
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225 >UniProtID:128UP_DROME|UniProtAcc:P32234|EMBL:AY069810 GTP-binding protein 128up - Drosophila melanogaster (Fruit fly)
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226
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227 will be converted into::
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228
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229 >UniProtAcc:P32234|UniProtID:128UP_DROME|EMBL:AY069810 GTP-binding protein 128up - Drosophila melanogaster (Fruit fly)
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230
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231 Specifying only *2,1* as the New order for the IDs will not work, because this header contains 3 IDs, \
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232 so you'll have to include the (new) position for the third one as well.
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233
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234 ========================================================
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235 *Need another type of conversion?*
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236 ========================================================
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237
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238 Contact your local bioinformaticians to add other conversions...
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239
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240 </help>
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241 </tool>
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