Mercurial > repos > artbio > sequence_format_converter

annotate sequence_format_converter.xml @ 1:871e3c96f84e 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 22:07:47 +0000
parents de21b6357ac1
children
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871e3c96f84e "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
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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2 <description></description>
1
871e3c96f84e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 9c5f0b8e89dfe4347c610f42923f0acad2ecc81b"
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3 <requirements>
871e3c96f84e "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>
871e3c96f84e "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
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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6 <command><![CDATA[
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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7 #if $input.is_of_type('fastq.gz'):
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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8 gzip -dc $input > '${input}.tmp';
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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9 python '$__tool_directory__'/sequence_format_converter.py
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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10 --input '${input}.tmp'
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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11 --output '$output'
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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12 --format '$output_format';
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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13 rm '${input}.tmp';
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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14 #else:
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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15 python '$__tool_directory__'/sequence_format_converter.py
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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16 --input '$input'
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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17 --output '$output'
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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18 --format '$output_format'
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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19 #end if
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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20 ]]></command>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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21
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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22 <inputs>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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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)"/>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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24 <param name="output_format" type="select" label="conversion options">
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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25 <option value="tabular" selected="true">tabular</option>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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26 <option value="fasta">Fasta</option>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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27 <option value="fastaw">Weighted fasta</option>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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28 </param>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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29 </inputs>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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30
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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31 <outputs>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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32 <data format="fasta" name="output" label="${output_format} conversion of ${input.name}">
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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33 <change_format>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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34 <when input="output_format" value="tabular" format="tabular"/>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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35 </change_format>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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36 </data>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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37 </outputs>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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38
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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39 <tests>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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40 <test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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41 <!-- convertion fasta to tabular -->
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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42 <param name="output_format" value="tabular" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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43 <param ftype="fasta" name="input" value="input.fa" />
1
871e3c96f84e "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
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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45 </test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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46 <test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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47 <!-- convertion tabular to fasta -->
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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48 <param name="output_format" value="fasta" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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49 <param ftype="tabular" name="input" value="output.tab" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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50 <output file="input.sorted.fa" name="output" sort="True"/>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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51 </test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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52 <test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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53 <!-- convertion fastaw to tabular -->
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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54 <param name="output_format" value="tabular" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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55 <param ftype="fasta" name="input" value="output.faw" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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56 <output file="output.sorted.tab" name="output" sort="True"/>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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57 </test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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58 <test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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59 <!-- convertion tabular to fastaw -->
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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60 <param name="output_format" value="fastaw" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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61 <param ftype="tabular" name="input" value="output.tab" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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62 <output file="output.sorted.faw" name="output" sort="True" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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63 </test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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64 <test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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65 <!-- convertion fasta to fastaw -->
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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66 <param name="output_format" value="fastaw" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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67 <param ftype="fasta" name="input" value="input.fa" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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68 <output file="output.sorted.faw" name="output" sort="True" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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69 </test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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70 <test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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71 <!-- convertion fastaw to fasta -->
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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72 <param name="output_format" value="fasta" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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73 <param ftype="fasta" name="input" value="output.faw" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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74 <output file="input.sorted.fa" name="output" sort="True" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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75 </test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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76 <test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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77 <!-- convertion fastq to tabular -->
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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78 <param name="output_format" value="tabular" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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79 <param ftype="fastq" name="input" value="input.fastqsanger" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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80 <output file="fastqTotabular.sorted.tab" name="output" sort="True" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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81 </test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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82 <test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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83 <!-- convertion fastq to fasta -->
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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84 <param name="output_format" value="fasta" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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85 <param ftype="fasta" name="input" value="input.fastqsanger" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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86 <output file="fastqTofasta.sorted.fa" name="output" sort="True" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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87 </test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
88 <test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
89 <!-- convertion fastq to fastaw -->
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
90 <param name="output_format" value="fastaw" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
91 <param ftype="fasta" name="input" value="input.fastqsanger" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
92 <output file="fastqTofastaw.sorted.faw" name="output" sort="True" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
93 </test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
94 <test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
95 <!-- convertion fastq.gz to tabular -->
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
96 <param name="output_format" value="tabular" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
97 <param ftype="fastq.gz" name="input" value="input.fastqsanger.gz" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
98 <output file="fastqTotabular.sorted.tab" name="output" sort="True" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
99 </test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
100 <test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
101 <!-- convertion fastq.gz to fasta -->
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
102 <param name="output_format" value="fasta" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
103 <param ftype="fastq.gz" name="input" value="input.fastqsanger.gz" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
104 <output file="fastqTofasta.sorted.fa" name="output" sort="True" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
105 </test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
106 <test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
107 <!-- convertion fastq.gz to fastaw -->
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
108 <param name="output_format" value="fastaw" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
109 <param ftype="fastq.gz" name="input" value="input.fastqsanger.gz" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
110 <output file="fastqTofastaw.sorted.faw" name="output" sort="True" />
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
111 </test>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
112 </tests>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
113
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
114
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
115 <help>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
116
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
117 **What it does**
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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118
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
119 The tool performs all pairwise conversions between sequence formats fasta, fastaw and tabular.
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
120
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
121 The tool is also able to convert fastq format in any of the formats fasta, fastaw and tabular.
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
122
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
123 The format of the input is automatically detected by the tool.
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
124
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
125 **Formats**
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
126
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
127 *Fasta*
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
128
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
129 >id1
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
130
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
131 ATGCATGACCAGATAGGAC
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
132
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
133 >id2
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
134
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
135 ATGCATGACCAGATAGGAC
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
136
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
137 Note that the tool handles fasta sequences over multiple lines
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
138
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
139
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
140 ----------
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
141
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
142 *Fastaw*
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
143
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
144 Allows to reduce the size of a fasta file of sequence reads:
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
145
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
146 >id1_n1
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
147
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
148 ATGCATGACCAGATAGGAC
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
149
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
150 >id2_n2
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
151
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
152 ATGCATGACCAGATAGGAC
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
153
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
154 etc...
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
155
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
156 Here n1 and n2 are integers that indicate the number of reads of the sequence found in the sequencing dataset
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
157
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
158 Note that if 2 fastaw files are merged (e.g. by concatenation), the values of the number of reads are wrong.
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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159
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
160 These values can simply be re-computed by submitting the merged file to a fastaw conversion with the *sequence_format_converter* tool !
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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161
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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162
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
163 ----------
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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164
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
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165 *Tabular*
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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166
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
167 Is a tabular version of fastaw without fasta headers:
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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168
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
169 column 1 column2
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
170
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
171 ATGCATGACCAGATAGGAC n1
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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172
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
173 ATGCATGACCAGATAGGAC n2
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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174
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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175
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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diff changeset
176 ----------
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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177
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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178 *Fastq*
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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179
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
parents:
diff changeset
180 @HWI-1
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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181
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
artbio
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182 ATGCATGACCAGATAGGAC
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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183
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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184 \+
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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185
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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186 BBBA;ACB9ABCBABB@@/
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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187
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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188 @HWI-2
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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189
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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190 ATGCATGACCAGATAGGAC
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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191
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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192 \+
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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193
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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194 ?03@?82?B>C@B>@CC?0
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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195
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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196
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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197 </help>
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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198
de21b6357ac1 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit 07c73df696d6d80e03f03232603d713882131625"
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199 </tool>