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comparison sequence_format_converter.xml @ 0:a8aacccd79a3 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
author artbio
date Mon, 04 Sep 2017 07:13:28 -0400
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1 <tool id="sequence_format_converter" name="sequence_format_converter" version="2.0.0">
2 <description></description>
3 <command><![CDATA[
4 python '$__tool_directory__'/sequence_format_converter.py
5 --input '$input'
6 --output '$output'
7 --format '$output_format'
8 ]]></command>
9
10 <inputs>
11 <param name="input" type="data" format="fasta, fastq, tabular" label="file to convert to tabular (input format is automatically detected)"/>
12 <param name="output_format" type="select" label="conversion options">
13 <option value="tabular" selected="true">tabular</option>
14 <option value="fasta">Fasta</option>
15 <option value="fastaw">Weighted fasta</option>
16 </param>
17 </inputs>
18
19 <outputs>
20 <data format="fasta" name="output" label="${output_format} conversion of ${input.name}">
21 <change_format>
22 <when input="output_format" value="tabular" format="tabular"/>
23 </change_format>
24 </data>
25 </outputs>
26
27 <tests>
28 <test>
29 <!-- convertion fasta to tabular -->
30 <param name="output_format" value="tabular" />
31 <param ftype="fasta" name="input" value="input.fa" />
32 <output file="output.tab" name="output" />
33 </test>
34 <test>
35 <!-- convertion tabular to fasta -->
36 <param name="output_format" value="fasta" />
37 <param ftype="tabular" name="input" value="output.tab" />
38 <output file="input.sorted.fa" name="output" sort="True"/>
39 </test>
40 <test>
41 <!-- convertion fastaw to tabular -->
42 <param name="output_format" value="tabular" />
43 <param ftype="fasta" name="input" value="output.faw" />
44 <output file="output.sorted.tab" name="output" sort="True"/>
45 </test>
46 <test>
47 <!-- convertion tabular to fastaw -->
48 <param name="output_format" value="fastaw" />
49 <param ftype="tabular" name="input" value="output.tab" />
50 <output file="output.sorted.faw" name="output" sort="True" />
51 </test>
52 <test>
53 <!-- convertion fasta to fastaw -->
54 <param name="output_format" value="fastaw" />
55 <param ftype="fasta" name="input" value="input.fa" />
56 <output file="output.sorted.faw" name="output" sort="True" />
57 </test>
58 <test>
59 <!-- convertion fastaw to fasta -->
60 <param name="output_format" value="fasta" />
61 <param ftype="fasta" name="input" value="output.faw" />
62 <output file="input.sorted.fa" name="output" sort="True" />
63 </test>
64 <test>
65 <!-- convertion fastq to tabular -->
66 <param name="output_format" value="tabular" />
67 <param ftype="fastq" name="input" value="input.fastqsanger" />
68 <output file="fastqTotabular.sorted.tab" name="output" sort="True" />
69 </test>
70 <test>
71 <!-- convertion fastq to fasta -->
72 <param name="output_format" value="fasta" />
73 <param ftype="fasta" name="input" value="input.fastqsanger" />
74 <output file="fastqTofasta.sorted.fa" name="output" sort="True" />
75 </test>
76 <test>
77 <!-- convertion fastq to fastaw -->
78 <param name="output_format" value="fastaw" />
79 <param ftype="fasta" name="input" value="input.fastqsanger" />
80 <output file="fastqTofastaw.sorted.faw" name="output" sort="True" />
81 </test>
82 </tests>
83
84
85 <help>
86
87 **What it does**
88
89 The tool performs all pairwise conversions between sequence formats fasta, fastaw and tabular.
90
91 The tool is also able to convert fastq format in any of the formats fasta, fastaw and tabular.
92
93 The format of the input is automatically detected by the tool.
94
95 **Formats**
96
97 *Fasta*
98
99 >id1
100
101 ATGCATGACCAGATAGGAC
102
103 >id2
104
105 ATGCATGACCAGATAGGAC
106
107 Note that the tool handles fasta sequences over multiple lines
108
109
110 ----------
111
112 *Fastaw*
113
114 Allows to reduce the size of a fasta file of sequence reads:
115
116 >id1_n1
117
118 ATGCATGACCAGATAGGAC
119
120 >id2_n2
121
122 ATGCATGACCAGATAGGAC
123
124 etc...
125
126 Here n1 and n2 are integers that indicate the number of reads of the sequence found in the sequencing dataset
127
128 Note that if 2 fastaw files are merged (e.g. by concatenation), the values of the number of reads are wrong.
129
130 These values can simply be re-computed by submitting the merged file to a fastaw conversion with the *sequence_format_converter* tool !
131
132
133 ----------
134
135 *Tabular*
136
137 Is a tabular version of fastaw without fasta headers:
138
139 column 1 column2
140
141 ATGCATGACCAGATAGGAC n1
142
143 ATGCATGACCAGATAGGAC n2
144
145
146 ----------
147
148 *Fastq*
149
150 @HWI-1
151
152 ATGCATGACCAGATAGGAC
153
154 \+
155
156 BBBA;ACB9ABCBABB@@/
157
158 @HWI-2
159
160 ATGCATGACCAGATAGGAC
161
162 \+
163
164 ?03@?82?B>C@B>@CC?0
165
166
167 </help>
168
169 </tool>