Mercurial > repos > artbio > sequence_format_converter

annotate sequence_format_converter.xml @ 4:1c14d2869d4d draft default tip

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 9c5f0b8e89dfe4347c610f42923f0acad2ecc81b"
author artbio
date Wed, 17 Mar 2021 22:09:13 +0000
parents 772bd67ef26a
children
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4
1c14d2869d4d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 9c5f0b8e89dfe4347c610f42923f0acad2ecc81b"
artbio
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1 <tool id="sequence_format_converter" name="sequence_format_converter" version="2.2.0">
0
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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2 <description></description>
4
1c14d2869d4d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 9c5f0b8e89dfe4347c610f42923f0acad2ecc81b"
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3 <requirements>
1c14d2869d4d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 9c5f0b8e89dfe4347c610f42923f0acad2ecc81b"
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4 <requirement type="package" version="3.7.6">python</requirement>
1c14d2869d4d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 9c5f0b8e89dfe4347c610f42923f0acad2ecc81b"
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5 </requirements>
0
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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6 <command><![CDATA[
1
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7 #if $input.is_of_type('fastq.gz'):
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8 gzip -dc $input > '${input}.tmp';
9ce7ccd468aa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit dfecfb40f245a3cdb09dd1cfe37be4cb164ad2eb
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9 python '$__tool_directory__'/sequence_format_converter.py
9ce7ccd468aa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit dfecfb40f245a3cdb09dd1cfe37be4cb164ad2eb
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10 --input '${input}.tmp'
9ce7ccd468aa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit dfecfb40f245a3cdb09dd1cfe37be4cb164ad2eb
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11 --output '$output'
9ce7ccd468aa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit dfecfb40f245a3cdb09dd1cfe37be4cb164ad2eb
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12 --format '$output_format';
9ce7ccd468aa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit dfecfb40f245a3cdb09dd1cfe37be4cb164ad2eb
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13 rm '${input}.tmp';
9ce7ccd468aa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit dfecfb40f245a3cdb09dd1cfe37be4cb164ad2eb
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14 #else:
0
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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15 python '$__tool_directory__'/sequence_format_converter.py
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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16 --input '$input'
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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17 --output '$output'
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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18 --format '$output_format'
1
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19 #end if
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20 ]]></command>
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21
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22 <inputs>
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23 <param name="input" type="data" format="fasta,fastq,tabular" label="file to convert to tabular (input format is automatically detected)"/>
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24 <param name="output_format" type="select" label="conversion options">
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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25 <option value="tabular" selected="true">tabular</option>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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26 <option value="fasta">Fasta</option>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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27 <option value="fastaw">Weighted fasta</option>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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28 </param>
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29 </inputs>
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30
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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31 <outputs>
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32 <data format="fasta" name="output" label="${output_format} conversion of ${input.name}">
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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33 <change_format>
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34 <when input="output_format" value="tabular" format="tabular"/>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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35 </change_format>
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36 </data>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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37 </outputs>
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38
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39 <tests>
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40 <test>
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41 <!-- convertion fasta to tabular -->
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42 <param name="output_format" value="tabular" />
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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43 <param ftype="fasta" name="input" value="input.fa" />
4
1c14d2869d4d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 9c5f0b8e89dfe4347c610f42923f0acad2ecc81b"
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44 <output file="output.tab" name="output" sort="true" />
0
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45 </test>
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46 <test>
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47 <!-- convertion tabular to fasta -->
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48 <param name="output_format" value="fasta" />
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49 <param ftype="tabular" name="input" value="output.tab" />
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50 <output file="input.sorted.fa" name="output" sort="True"/>
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51 </test>
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52 <test>
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53 <!-- convertion fastaw to tabular -->
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54 <param name="output_format" value="tabular" />
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55 <param ftype="fasta" name="input" value="output.faw" />
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56 <output file="output.sorted.tab" name="output" sort="True"/>
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57 </test>
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58 <test>
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59 <!-- convertion tabular to fastaw -->
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60 <param name="output_format" value="fastaw" />
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61 <param ftype="tabular" name="input" value="output.tab" />
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62 <output file="output.sorted.faw" name="output" sort="True" />
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63 </test>
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64 <test>
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65 <!-- convertion fasta to fastaw -->
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66 <param name="output_format" value="fastaw" />
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67 <param ftype="fasta" name="input" value="input.fa" />
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68 <output file="output.sorted.faw" name="output" sort="True" />
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69 </test>
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70 <test>
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71 <!-- convertion fastaw to fasta -->
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72 <param name="output_format" value="fasta" />
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73 <param ftype="fasta" name="input" value="output.faw" />
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74 <output file="input.sorted.fa" name="output" sort="True" />
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75 </test>
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76 <test>
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77 <!-- convertion fastq to tabular -->
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78 <param name="output_format" value="tabular" />
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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79 <param ftype="fastq" name="input" value="input.fastqsanger" />
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80 <output file="fastqTotabular.sorted.tab" name="output" sort="True" />
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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81 </test>
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82 <test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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83 <!-- convertion fastq to fasta -->
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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84 <param name="output_format" value="fasta" />
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85 <param ftype="fasta" name="input" value="input.fastqsanger" />
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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86 <output file="fastqTofasta.sorted.fa" name="output" sort="True" />
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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87 </test>
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88 <test>
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89 <!-- convertion fastq to fastaw -->
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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90 <param name="output_format" value="fastaw" />
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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91 <param ftype="fasta" name="input" value="input.fastqsanger" />
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92 <output file="fastqTofastaw.sorted.faw" name="output" sort="True" />
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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93 </test>
1
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94 <test>
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95 <!-- convertion fastq.gz to tabular -->
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96 <param name="output_format" value="tabular" />
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97 <param ftype="fastq.gz" name="input" value="input.fastqsanger.gz" />
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98 <output file="fastqTotabular.sorted.tab" name="output" sort="True" />
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99 </test>
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100 <test>
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101 <!-- convertion fastq.gz to fasta -->
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102 <param name="output_format" value="fasta" />
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103 <param ftype="fastq.gz" name="input" value="input.fastqsanger.gz" />
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104 <output file="fastqTofasta.sorted.fa" name="output" sort="True" />
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105 </test>
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106 <test>
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107 <!-- convertion fastq.gz to fastaw -->
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108 <param name="output_format" value="fastaw" />
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109 <param ftype="fastq.gz" name="input" value="input.fastqsanger.gz" />
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110 <output file="fastqTofastaw.sorted.faw" name="output" sort="True" />
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111 </test>
0
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112 </tests>
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113
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114
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115 <help>
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116
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117 **What it does**
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118
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119 The tool performs all pairwise conversions between sequence formats fasta, fastaw and tabular.
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120
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121 The tool is also able to convert fastq format in any of the formats fasta, fastaw and tabular.
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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122
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123 The format of the input is automatically detected by the tool.
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124
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125 **Formats**
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126
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127 *Fasta*
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128
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129 >id1
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130
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131 ATGCATGACCAGATAGGAC
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132
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133 >id2
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134
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135 ATGCATGACCAGATAGGAC
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136
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137 Note that the tool handles fasta sequences over multiple lines
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138
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139
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140 ----------
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141
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142 *Fastaw*
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143
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144 Allows to reduce the size of a fasta file of sequence reads:
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145
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146 >id1_n1
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147
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148 ATGCATGACCAGATAGGAC
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149
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150 >id2_n2
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151
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152 ATGCATGACCAGATAGGAC
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153
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154 etc...
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155
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156 Here n1 and n2 are integers that indicate the number of reads of the sequence found in the sequencing dataset
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157
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158 Note that if 2 fastaw files are merged (e.g. by concatenation), the values of the number of reads are wrong.
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159
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160 These values can simply be re-computed by submitting the merged file to a fastaw conversion with the *sequence_format_converter* tool !
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161
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162
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163 ----------
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164
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165 *Tabular*
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166
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167 Is a tabular version of fastaw without fasta headers:
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168
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169 column 1 column2
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170
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171 ATGCATGACCAGATAGGAC n1
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172
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173 ATGCATGACCAGATAGGAC n2
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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 *Fastq*
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179
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180 @HWI-1
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181
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182 ATGCATGACCAGATAGGAC
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183
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184 \+
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185
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186 BBBA;ACB9ABCBABB@@/
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187
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188 @HWI-2
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189
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190 ATGCATGACCAGATAGGAC
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191
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192 \+
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193
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194 ?03@?82?B>C@B>@CC?0
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195
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196
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197 </help>
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198
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199 </tool>