Mercurial > repos > itaxotools > dna_convert

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author itaxotools
date Sun, 29 Jan 2023 16:32:28 +0000
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1 <tool id="DNAconvert" name="DNAconvert" version="0.2.0" python_template_version="3.5" profile="21.05">
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2 <description>Converts genetic sequences between different formats</description>
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3 <requirements>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[$__tool_directory__/DNAconvert '$input1' '$output1' '--cmd'
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6 #if $allow_empty_sequences:
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7 --allow_empty_sequence
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8 #end if
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9 #if $disable_automatic_renaming:
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10 --disable_automatic_renaming
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11 #end if
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12 --informat '$informat1'
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13 --outformat '$outformat_and_extension.outformat1' ]]>
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14 </command>
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15 <inputs>
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16 <param type="data" name="input1" label="Source file" format="data" />
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17 <param name="informat1" type="select" label="Input Format">
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18 <option value="tab">Internal tab format</option>
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19 <option value="tab_noheaders">Internal tab format without headers</option>
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20 <option value="fasta">FASTA format</option>
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21 <option value="fasta_hapview">FASTA format for Haplotype Viewer</option>
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22 <option value="fasta_gbexport">FASTA format for export into Genbank repository</option>
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23 <option value="mold_fasta">FASTA format with sequence name matching requirements for the tool MolD</option>
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24 <option value="fastq">FASTQ format</option>
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25 <option value="phylip">Phylip format</option>
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26 <option value="relaxed_phylip">relaxed Phylip format</option>
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27 <option value="nexus">NEXUS format</option>
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28 <option value="nexml">DnaCharacterMatrix in NeXML format</option>
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29 <option value="genbank">Genbank flat file format</option>
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30 </param>
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31 <conditional name="outformat_and_extension">
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32 <param name="outformat1" type="select" label="Output Format">
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33 <option value="tab">Internal tab format</option>
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34 <option value="tab_noheaders">Internal tab format without headers</option>
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35 <option value="fasta">FASTA format</option>
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36 <option value="fasta_hapview">FASTA format for Haplotype Viewer</option>
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37 <option value="fasta_gbexport">FASTA format for export into Genbank repository</option>
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38 <option value="mold_fasta">FASTA format with sequence name matching requirements for the tool MolD</option>
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39 <option value="fastq">FASTQ format</option>
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40 <option value="phylip">Phylip format</option>
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41 <option value="relaxed_phylip">relaxed Phylip format</option>
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42 <option value="nexus">NEXUS format</option>
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43 <option value="nexml">DnaCharacterMatrix in NeXML format</option>
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44 <option value="genbank">Genbank flat file format</option>
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45 </param>
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46 <when value="tab">
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47 <param name="extension1" type="hidden" value="tab"/>
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48 </when>
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49 <when value="phylip">
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50 <param name="extension1" type="hidden" value="phy"/>
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51 </when>
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52 <when value="fasta">
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53 <param name="extension1" type="hidden" value="fas"/>
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54 </when>
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55 <when value="fasta_hapview">
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56 <param name="extension1" type="hidden" value="fas"/>
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57 </when>
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58 <when value="fasta_gbexport">
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59 <param name="extension1" type="hidden" value="fas"/>
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60 </when>
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61 <when value="mold_fasta">
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62 <param name="extension1" type="hidden" value="fas"/>
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63 </when>
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64 <when value="fastq">
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65 <param name="extension1" type="hidden" value="fq"/>
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66 </when>
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67 <when value="tab_noheaders">
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68 <param name="extension1" type="hidden" value="tab"/>
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69 </when>
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70 <when value="relaxed_phylip">
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71 <param name="extension1" type="hidden" value="phy"/>
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72 </when>
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73 <when value="nexus">
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74 <param name="extension1" type="hidden" value="nex"/>
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75 </when>
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76 <when value="nexml">
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77 <param name="extension1" type="hidden" value="xml"/>
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78 </when>
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79 <when value="genbank">
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80 <param name="extension1" type="hidden" value="gb"/>
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81 </when>
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82 </conditional>
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83
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84 <param name="allow_empty_sequences" type="boolean" label="Allow empty sequences" help="set this to keep the empty sequences in the output file" />
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85 <param name="disable_automatic_renaming" type="boolean" label="Disable automatic renaming" help="disables automatic renaming, may result in duplicate sequence names in Phylip and Nexus files" />
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86 </inputs>
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87 <outputs>
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88 <data name="output1" label="${os.path.splitext(os.path.basename($input1.name))[0]}.${outformat_and_extension.extension1}" metadata_source="input1" format="tabular">
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89 <change_format>
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90 <when input="outformat_and_extension.outformat1" value="phylip" format="phylip" />
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91 <when input="outformat_and_extension.outformat1" value="fasta" format="fasta" />
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92 <when input="outformat_and_extension.outformat1" value="tab_noheaders" format="tabular" />
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93 <when input="outformat_and_extension.outformat1" value="tab" format="tabular" />
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94 <when input="outformat_and_extension.outformat1" value="fasta_hapview" format="fasta" />
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95 <when input="outformat_and_extension.outformat1" value="fastq" format="fastq" />
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96 <when input="outformat_and_extension.outformat1" value="relaxed_phylip" format="phylip" />
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97 <when input="outformat_and_extension.outformat1" value="nexus" format="nexus" />
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98 <when input="outformat_and_extension.outformat1" value="nexml" format="nexml" />
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99 <when input="outformat_and_extension.outformat1" value="genbank" format="gb" />
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100 <when input="outformat_and_extension.outformat1" value="mold_fasta" format="fasta" />
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101 </change_format>
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102 </data>
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103 </outputs>
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104 <tests>
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105 <test>
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106 <param name="input1" value="DNAconvert_examplefile2_iTaxoTools_0_1.fas"/>
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107 <param name="informat1" value="fasta" />
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108 <param name="outformat1" value="tab" />
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109 <output name="output1" file="DNAtestout_1.tab"/>
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110 </test>
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111 <test>
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112 <param name="input1" value="DNAconvert_examplefile3_iTaxoTools_0_1.tab"/>
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113 <param name="informat1" value="tab" />
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114 <param name="outformat1" value="phylip" />
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115 <output name="output1" file="DNAtestout_2.phy"/>
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116 </test>
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117 </tests>
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118 <help><![CDATA[
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119
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120 **DNAconvert**
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121
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122 A program to convert between different file formats containing DNA sequences.
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123 Written by V. Kharchev in the framework of the iTaxoTools project.
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124 Galaxy wrapper for DNAconvert 0.1 written in 2022/2023 by F. Fischell.
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125
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126 Standalone executables with graphical user interface of the newest version of ASAP for Windows and Mac are available from:
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127
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128 http://itaxotools.org/
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129
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130 https://github.com/iTaxoTools/iTaxoTools-Executables/releases
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131
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132
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133 For more information, see the iTaxoTools manual available at:
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134 http://itaxotools.org/
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135
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136 **Usage**
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137
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138 - Specify an input file and the input file format, as well as the desired output file format.
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139 - DNAconvert will "sanitize" sequence names by replacing special characters by underscores
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140 - For formats that require unique sequence names, DNAconvert can automatically rename sequnces by adding consecutive numbers to the names
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141 - An important feature of DNAconvert is the option to use tab-delimited files which allows curating sequence data sets with metadata in spreadsheet editors. Refer to the iTaxoTool manual for details.
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142
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143 **Supported formats**
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144
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145 * `tab` = tsv: [Internal tab format][1] = tab-delimited text
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146
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147 * `tab_noheaders`: [Internal tab format][1] without headers = tab-delimited text without headers
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148
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149 * `fasta`: FASTA format
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150
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151 * `phylip`: Phylip format
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152
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153 * `relaxed_phylip`: relaxed Phylip format (with no restriction on the length of sequence names)
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154
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155 * `fasta_hapview`: FASTA format with sequence names formatted for Haplotype Viewer
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156
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157 * `fastq`: FASTQ format
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158
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159 * `fasta_gbexport`: FASTA format with sequence names adjusted for export into GenBank repository
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160
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161 * `nexus`: NEXUS format
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162
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163 * `nexml`: DnaCharacterMatrix in NeXML format
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164
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165 * `genbank`: Genbank flat file format
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166
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167 * `mold_fasta`: FASTA format with sequence name matching requirements for the tool MolD *
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168
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169
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170 **Recognised extension**
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171
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172 Automatic recognition of file format based on extension in file name not yet available in the Galaxy implementation.
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173
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174
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175
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176
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177
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178 ]]></help>
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179 <citations>
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180 <citation type="doi">
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181 10.11646/megataxa.6.2.1
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182 </citation>
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183 </citations>
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184 </tool>