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annotate fasta_tabular_converter.xml @ 1:2f7278120be9 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f
author drosofff
date Tue, 22 Mar 2016 18:54:00 -0400
parents 951cb6b3979b
children 36388b666bfc
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2f7278120be9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f
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1 <tool id="fasta_tabular_converter" name="fasta - tabular" version="1.1.0">
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2 <description>conversions</description>
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3 <command interpreter="python">fasta_tabular_converter.py
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4 --input $input
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5 --output $output
2f7278120be9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f
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6 --type $switch.conversionType
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7 </command>
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8 <inputs>
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9 <conditional name="switch">
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10 <param name="conversionType" type="select" label="conversion option">
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11 <option value="fasta2tabular" selected="true">fasta to tabular</option>
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12 <option value="tabular2fasta">tabular to fasta</option>
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13 <option value="tabular2fastaweight">tabular to weighted fasta</option>
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14 <option value="fastaweight2fastaweight">recompile weighted fasta to catenated fasta weighted</option>
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15 <option value="fastaweight2fasta">fasta weighted to fasta</option>
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16 </param>
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17 <when value="fasta2tabular">
2f7278120be9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f
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18 <param name="input" type="data" format="fasta" label="fasta file to convert to tabular"/>
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19 </when>
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20 <when value="tabular2fasta">
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21 <param name="input" type="data" format="tabular" label="tabular file to convert to fasta"/>
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22 </when>
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23 <when value="tabular2fastaweight">
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24 <param name="input" type="data" format="tabular" label="tabular file to convert to fasta weighted"/>
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25 </when>
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26 <when value="fastaweight2fastaweight">
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27 <param name="input" type="data" format="fasta" label="catenated fasta weighted to recompile" help="Use this option only if you known what you're doing"/>
2f7278120be9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f
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28 </when>
2f7278120be9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f
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29 <when value="fastaweight2fasta">
2f7278120be9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f
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30 <param name="input" type="data" format="fasta" label="fasta weighted file to convert to fasta"/>
2f7278120be9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f
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31 </when>
2f7278120be9 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_fasta_tabular_converter commit 6a93f2809e2939f9d847c3238bfbff8ead367d9f
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32 </conditional>
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33 </inputs>
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34
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35 <outputs>
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36 <data format="fasta" name="output" label="${switch.conversionType} conversion">
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37 <change_format>
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38 <when input="switch.conversionType" value="fasta2tabular" format="tabular"/>
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39 <when input="switch.conversionType" value="fastaweight2fastaweight" format="fasta"/>
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40 <when input="switch.conversionType" value="fastaweight2fasta" format="fasta"/>
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41 </change_format>
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42 </data>
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43 </outputs>
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44
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45 <tests>
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46 <test>
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47 <param name="conversionType" value="fasta2tabular" />
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48 <param ftype="fasta" name="input" value="input.fa" />
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49 <output file="output.tab" name="output" />
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50 </test>
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51 <test>
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52 <param name="conversionType" value="tabular2fastaweight" />
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53 <param ftype="tabular" name="input" value="output.tab" />
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54 <output file="output.faw" name="output" />
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55 </test>
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56 </tests>
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57
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58
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59 <help>
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60
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61 **What it does**
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62
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63 Converts fasta files to tabular files with sequence on first column and occurence of the sequence in the second column; and reciprocally.
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64
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65 This format is suitable for storage of sequence datasets in the data library, and will be used in the future.
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66
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67 Regeneration of the original fasta file from the tabular format is ensured by the same tool
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68
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69 This tool also handle a fasta "weigthed" format with headers as:
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70 >id_numberofreads
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71 ATGCATGACCAGATAGGAC
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72 etc...
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73
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74 with generation of the "weigthed" format from a tabular format, and recompilation of catenated weighted fasta files
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75
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76 </help>
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77
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78 </tool>