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planemo upload commit 232ce39054ce38be27c436a4cabec2800e14f988-dirty
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">
2 <description>Converts genetic sequences between different formats</description>
3 <requirements>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[$__tool_directory__/DNAconvert '$input1' '$output1' '--cmd'
6 #if $allow_empty_sequences:
7 --allow_empty_sequence
8 #end if
9 #if $disable_automatic_renaming:
10 --disable_automatic_renaming
11 #end if
12 --informat '$informat1'
13 --outformat '$outformat_and_extension.outformat1' ]]>
14 </command>
15 <inputs>
16 <param type="data" name="input1" label="Source file" format="data" />
17 <param name="informat1" type="select" label="Input Format">
18 <option value="tab">Internal tab format</option>
19 <option value="tab_noheaders">Internal tab format without headers</option>
20 <option value="fasta">FASTA format</option>
21 <option value="fasta_hapview">FASTA format for Haplotype Viewer</option>
22 <option value="fasta_gbexport">FASTA format for export into Genbank repository</option>
23 <option value="mold_fasta">FASTA format with sequence name matching requirements for the tool MolD</option>
24 <option value="fastq">FASTQ format</option>
25 <option value="phylip">Phylip format</option>
26 <option value="relaxed_phylip">relaxed Phylip format</option>
27 <option value="nexus">NEXUS format</option>
28 <option value="nexml">DnaCharacterMatrix in NeXML format</option>
29 <option value="genbank">Genbank flat file format</option>
30 </param>
31 <conditional name="outformat_and_extension">
32 <param name="outformat1" type="select" label="Output Format">
33 <option value="tab">Internal tab format</option>
34 <option value="tab_noheaders">Internal tab format without headers</option>
35 <option value="fasta">FASTA format</option>
36 <option value="fasta_hapview">FASTA format for Haplotype Viewer</option>
37 <option value="fasta_gbexport">FASTA format for export into Genbank repository</option>
38 <option value="mold_fasta">FASTA format with sequence name matching requirements for the tool MolD</option>
39 <option value="fastq">FASTQ format</option>
40 <option value="phylip">Phylip format</option>
41 <option value="relaxed_phylip">relaxed Phylip format</option>
42 <option value="nexus">NEXUS format</option>
43 <option value="nexml">DnaCharacterMatrix in NeXML format</option>
44 <option value="genbank">Genbank flat file format</option>
45 </param>
46 <when value="tab">
47 <param name="extension1" type="hidden" value="tab"/>
48 </when>
49 <when value="phylip">
50 <param name="extension1" type="hidden" value="phy"/>
51 </when>
52 <when value="fasta">
53 <param name="extension1" type="hidden" value="fas"/>
54 </when>
55 <when value="fasta_hapview">
56 <param name="extension1" type="hidden" value="fas"/>
57 </when>
58 <when value="fasta_gbexport">
59 <param name="extension1" type="hidden" value="fas"/>
60 </when>
61 <when value="mold_fasta">
62 <param name="extension1" type="hidden" value="fas"/>
63 </when>
64 <when value="fastq">
65 <param name="extension1" type="hidden" value="fq"/>
66 </when>
67 <when value="tab_noheaders">
68 <param name="extension1" type="hidden" value="tab"/>
69 </when>
70 <when value="relaxed_phylip">
71 <param name="extension1" type="hidden" value="phy"/>
72 </when>
73 <when value="nexus">
74 <param name="extension1" type="hidden" value="nex"/>
75 </when>
76 <when value="nexml">
77 <param name="extension1" type="hidden" value="xml"/>
78 </when>
79 <when value="genbank">
80 <param name="extension1" type="hidden" value="gb"/>
81 </when>
82 </conditional>
83
84 <param name="allow_empty_sequences" type="boolean" label="Allow empty sequences" help="set this to keep the empty sequences in the output file" />
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" />
86 </inputs>
87 <outputs>
88 <data name="output1" label="${os.path.splitext(os.path.basename($input1.name))[0]}.${outformat_and_extension.extension1}" metadata_source="input1" format="tabular">
89 <change_format>
90 <when input="outformat_and_extension.outformat1" value="phylip" format="phylip" />
91 <when input="outformat_and_extension.outformat1" value="fasta" format="fasta" />
92 <when input="outformat_and_extension.outformat1" value="tab_noheaders" format="tabular" />
93 <when input="outformat_and_extension.outformat1" value="tab" format="tabular" />
94 <when input="outformat_and_extension.outformat1" value="fasta_hapview" format="fasta" />
95 <when input="outformat_and_extension.outformat1" value="fastq" format="fastq" />
96 <when input="outformat_and_extension.outformat1" value="relaxed_phylip" format="phylip" />
97 <when input="outformat_and_extension.outformat1" value="nexus" format="nexus" />
98 <when input="outformat_and_extension.outformat1" value="nexml" format="nexml" />
99 <when input="outformat_and_extension.outformat1" value="genbank" format="gb" />
100 <when input="outformat_and_extension.outformat1" value="mold_fasta" format="fasta" />
101 </change_format>
102 </data>
103 </outputs>
104 <tests>
105 <test>
106 <param name="input1" value="DNAconvert_examplefile2_iTaxoTools_0_1.fas"/>
107 <param name="informat1" value="fasta" />
108 <param name="outformat1" value="tab" />
109 <output name="output1" file="DNAtestout_1.tab"/>
110 </test>
111 <test>
112 <param name="input1" value="DNAconvert_examplefile3_iTaxoTools_0_1.tab"/>
113 <param name="informat1" value="tab" />
114 <param name="outformat1" value="phylip" />
115 <output name="output1" file="DNAtestout_2.phy"/>
116 </test>
117 </tests>
118 <help><![CDATA[
119
120 **DNAconvert**
121
122 A program to convert between different file formats containing DNA sequences.
123 Written by V. Kharchev in the framework of the iTaxoTools project.
124 Galaxy wrapper for DNAconvert 0.1 written in 2022/2023 by F. Fischell.
125
126 Standalone executables with graphical user interface of the newest version of ASAP for Windows and Mac are available from:
127
128 http://itaxotools.org/
129
130 https://github.com/iTaxoTools/iTaxoTools-Executables/releases
131
132
133 For more information, see the iTaxoTools manual available at:
134 http://itaxotools.org/
135
136 **Usage**
137
138 - Specify an input file and the input file format, as well as the desired output file format.
139 - DNAconvert will "sanitize" sequence names by replacing special characters by underscores
140 - For formats that require unique sequence names, DNAconvert can automatically rename sequnces by adding consecutive numbers to the names
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.
142
143 **Supported formats**
144
145 * `tab` = tsv: [Internal tab format][1] = tab-delimited text
146
147 * `tab_noheaders`: [Internal tab format][1] without headers = tab-delimited text without headers
148
149 * `fasta`: FASTA format
150
151 * `phylip`: Phylip format
152
153 * `relaxed_phylip`: relaxed Phylip format (with no restriction on the length of sequence names)
154
155 * `fasta_hapview`: FASTA format with sequence names formatted for Haplotype Viewer
156
157 * `fastq`: FASTQ format
158
159 * `fasta_gbexport`: FASTA format with sequence names adjusted for export into GenBank repository
160
161 * `nexus`: NEXUS format
162
163 * `nexml`: DnaCharacterMatrix in NeXML format
164
165 * `genbank`: Genbank flat file format
166
167 * `mold_fasta`: FASTA format with sequence name matching requirements for the tool MolD *
168
169
170 **Recognised extension**
171
172 Automatic recognition of file format based on extension in file name not yet available in the Galaxy implementation.
173
174
175
176
177
178 ]]></help>
179 <citations>
180 <citation type="doi">
181 10.11646/megataxa.6.2.1
182 </citation>
183 </citations>
184 </tool>