Mercurial > repos > artbio > sequence_format_converter

annotate sequence_format_converter.xml @ 3:772bd67ef26a draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
author artbio
date Mon, 11 May 2020 19:58:45 -0400
parents f1d59113125a
children 1c14d2869d4d
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3
772bd67ef26a "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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1 <tool id="sequence_format_converter" name="sequence_format_converter" version="2.1.2">
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>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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3 <command><![CDATA[
1
9ce7ccd468aa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit dfecfb40f245a3cdb09dd1cfe37be4cb164ad2eb
artbio
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4 #if $input.is_of_type('fastq.gz'):
9ce7ccd468aa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit dfecfb40f245a3cdb09dd1cfe37be4cb164ad2eb
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5 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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6 python '$__tool_directory__'/sequence_format_converter.py
9ce7ccd468aa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit dfecfb40f245a3cdb09dd1cfe37be4cb164ad2eb
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7 --input '${input}.tmp'
9ce7ccd468aa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit dfecfb40f245a3cdb09dd1cfe37be4cb164ad2eb
artbio
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8 --output '$output'
9ce7ccd468aa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit dfecfb40f245a3cdb09dd1cfe37be4cb164ad2eb
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9 --format '$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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10 rm '${input}.tmp';
9ce7ccd468aa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit dfecfb40f245a3cdb09dd1cfe37be4cb164ad2eb
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11 #else:
0
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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12 python '$__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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13 --input '$input'
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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14 --output '$output'
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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15 --format '$output_format'
1
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16 #end if
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17 ]]></command>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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18
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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19 <inputs>
2
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20 <param name="input" type="data" format="fasta,fastq,tabular" label="file to convert to tabular (input format is automatically detected)"/>
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a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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21 <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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22 <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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23 <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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24 <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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25 </param>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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26 </inputs>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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27
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28 <outputs>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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29 <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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30 <change_format>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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31 <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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32 </change_format>
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33 </data>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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34 </outputs>
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35
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36 <tests>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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37 <test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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38 <!-- convertion fasta to tabular -->
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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39 <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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40 <param ftype="fasta" name="input" value="input.fa" />
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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41 <output file="output.tab" name="output" />
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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42 </test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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43 <test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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44 <!-- convertion tabular 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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45 <param name="output_format" value="fasta" />
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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46 <param ftype="tabular" name="input" value="output.tab" />
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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47 <output file="input.sorted.fa" name="output" sort="True"/>
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48 </test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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49 <test>
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50 <!-- convertion fastaw to tabular -->
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51 <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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52 <param ftype="fasta" name="input" value="output.faw" />
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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53 <output file="output.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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54 </test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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55 <test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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56 <!-- convertion tabular 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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57 <param name="output_format" value="fastaw" />
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58 <param ftype="tabular" name="input" value="output.tab" />
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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59 <output file="output.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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60 </test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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61 <test>
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62 <!-- convertion fasta to fastaw -->
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63 <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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64 <param ftype="fasta" name="input" value="input.fa" />
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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65 <output file="output.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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66 </test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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67 <test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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68 <!-- convertion fastaw to fasta -->
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69 <param name="output_format" value="fasta" />
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70 <param ftype="fasta" name="input" value="output.faw" />
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71 <output file="input.sorted.fa" name="output" sort="True" />
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72 </test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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73 <test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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74 <!-- convertion fastq to tabular -->
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75 <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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76 <param ftype="fastq" 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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77 <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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78 </test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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79 <test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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80 <!-- 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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81 <param name="output_format" value="fasta" />
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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82 <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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83 <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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84 </test>
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85 <test>
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86 <!-- convertion fastq to fastaw -->
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87 <param name="output_format" value="fastaw" />
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88 <param ftype="fasta" name="input" value="input.fastqsanger" />
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89 <output file="fastqTofastaw.sorted.faw" name="output" sort="True" />
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90 </test>
1
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91 <test>
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92 <!-- convertion fastq.gz to tabular -->
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93 <param name="output_format" value="tabular" />
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94 <param ftype="fastq.gz" name="input" value="input.fastqsanger.gz" />
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95 <output file="fastqTotabular.sorted.tab" name="output" sort="True" />
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96 </test>
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97 <test>
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98 <!-- convertion fastq.gz to fasta -->
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99 <param name="output_format" value="fasta" />
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100 <param ftype="fastq.gz" name="input" value="input.fastqsanger.gz" />
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101 <output file="fastqTofasta.sorted.fa" name="output" sort="True" />
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102 </test>
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103 <test>
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104 <!-- convertion fastq.gz to fastaw -->
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105 <param name="output_format" value="fastaw" />
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106 <param ftype="fastq.gz" name="input" value="input.fastqsanger.gz" />
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107 <output file="fastqTofastaw.sorted.faw" name="output" sort="True" />
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108 </test>
0
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109 </tests>
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110
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111
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112 <help>
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113
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114 **What it does**
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115
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116 The tool performs all pairwise conversions between sequence formats fasta, fastaw and tabular.
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117
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118 The tool is also able to convert fastq format in any of the formats fasta, fastaw and tabular.
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119
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120 The format of the input is automatically detected by the tool.
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121
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122 **Formats**
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123
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124 *Fasta*
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125
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126 >id1
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127
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128 ATGCATGACCAGATAGGAC
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129
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130 >id2
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131
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132 ATGCATGACCAGATAGGAC
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133
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134 Note that the tool handles fasta sequences over multiple lines
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135
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136
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137 ----------
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138
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139 *Fastaw*
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140
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141 Allows to reduce the size of a fasta file of sequence reads:
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142
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143 >id1_n1
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144
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145 ATGCATGACCAGATAGGAC
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146
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147 >id2_n2
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148
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149 ATGCATGACCAGATAGGAC
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150
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151 etc...
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152
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153 Here n1 and n2 are integers that indicate the number of reads of the sequence found in the sequencing dataset
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154
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155 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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156
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157 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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158
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159
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160 ----------
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161
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162 *Tabular*
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163
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164 Is a tabular version of fastaw without fasta headers:
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165
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166 column 1 column2
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167
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168 ATGCATGACCAGATAGGAC n1
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169
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170 ATGCATGACCAGATAGGAC n2
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171
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172
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173 ----------
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174
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175 *Fastq*
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176
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177 @HWI-1
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178
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179 ATGCATGACCAGATAGGAC
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180
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181 \+
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182
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183 BBBA;ACB9ABCBABB@@/
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184
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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185 @HWI-2
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186
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187 ATGCATGACCAGATAGGAC
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189 \+
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190
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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191 ?03@?82?B>C@B>@CC?0
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192
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193
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194 </help>
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196 </tool>