Mercurial > repos > artbio > sequence_format_converter

annotate sequence_format_converter.xml @ 0:a8aacccd79a3 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
author artbio
date Mon, 04 Sep 2017 07:13:28 -0400
parents
children 9ce7ccd468aa
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0
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
artbio
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1 <tool id="sequence_format_converter" name="sequence_format_converter" version="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>
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[
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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4 python '$__tool_directory__'/sequence_format_converter.py
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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5 --input '$input'
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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6 --output '$output'
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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7 --format '$output_format'
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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8 ]]></command>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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9
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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10 <inputs>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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11 <param name="input" type="data" format="fasta, fastq, tabular" label="file to convert to tabular (input format is automatically detected)"/>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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12 <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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13 <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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14 <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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15 <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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16 </param>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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17 </inputs>
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 <outputs>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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20 <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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21 <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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22 <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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23 </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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24 </data>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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25 </outputs>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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26
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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27 <tests>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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28 <test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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29 <!-- 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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30 <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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31 <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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32 <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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33 </test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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34 <test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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35 <!-- 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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36 <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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37 <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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38 <output file="input.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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39 </test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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40 <test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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41 <!-- convertion fastaw 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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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="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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44 <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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45 </test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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46 <test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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47 <!-- 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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48 <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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49 <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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50 <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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51 </test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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52 <test>
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53 <!-- convertion fasta 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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54 <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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55 <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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56 <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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57 </test>
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58 <test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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59 <!-- convertion fastaw 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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60 <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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61 <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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62 <output file="input.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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63 </test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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64 <test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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65 <!-- convertion fastq to tabular -->
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66 <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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67 <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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68 <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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69 </test>
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70 <test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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71 <!-- 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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72 <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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73 <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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74 <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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75 </test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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76 <test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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77 <!-- 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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78 <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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79 <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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80 <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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81 </test>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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82 </tests>
a8aacccd79a3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sequence_format_converter commit d6ef80f9db43eae4f58b33f58b5ef6f8209907db
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83
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84
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85 <help>
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86
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87 **What it does**
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88
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89 The tool performs all pairwise conversions between sequence formats fasta, fastaw and tabular.
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90
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91 The tool is also able to convert fastq format in any of the formats fasta, fastaw and tabular.
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92
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93 The format of the input is automatically detected by the tool.
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94
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95 **Formats**
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96
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97 *Fasta*
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98
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99 >id1
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100
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101 ATGCATGACCAGATAGGAC
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102
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103 >id2
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104
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105 ATGCATGACCAGATAGGAC
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106
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107 Note that the tool handles fasta sequences over multiple lines
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108
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109
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110 ----------
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111
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112 *Fastaw*
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113
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114 Allows to reduce the size of a fasta file of sequence reads:
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115
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116 >id1_n1
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117
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118 ATGCATGACCAGATAGGAC
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119
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120 >id2_n2
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121
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122 ATGCATGACCAGATAGGAC
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123
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124 etc...
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125
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126 Here n1 and n2 are integers that indicate the number of reads of the sequence found in the sequencing dataset
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127
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128 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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129
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130 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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131
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132
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133 ----------
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134
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135 *Tabular*
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136
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137 Is a tabular version of fastaw without fasta headers:
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138
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139 column 1 column2
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140
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141 ATGCATGACCAGATAGGAC n1
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142
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143 ATGCATGACCAGATAGGAC n2
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144
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145
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146 ----------
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147
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148 *Fastq*
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149
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150 @HWI-1
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151
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152 ATGCATGACCAGATAGGAC
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153
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154 \+
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155
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156 BBBA;ACB9ABCBABB@@/
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157
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158 @HWI-2
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159
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160 ATGCATGACCAGATAGGAC
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161
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162 \+
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163
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164 ?03@?82?B>C@B>@CC?0
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165
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166
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167 </help>
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168
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169 </tool>