Mercurial > repos > drosofff > msp_fasta_tabular_converter

annotate fasta_tabular_converter.xml @ 0:951cb6b3979b draft

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author drosofff
date Sun, 21 Jun 2015 14:28:49 -0400
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children 2f7278120be9
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951cb6b3979b planemo upload for repository https://bitbucket.org/drosofff/gedtools/
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1 <tool id="fasta_tabular_converter" name="fasta - tabular" version="1.0.2">
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2 <description>conversions</description>
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3 <command interpreter="python">fasta_tabular_converter.py $input $output $switch.conversionType</command>
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4 <inputs>
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5 <conditional name="switch">
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6 <param name="conversionType" type="select" label="conversion option">
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7 <option value="fasta2tabular" selected="true">fasta to tabular</option>
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8 <option value="tabular2fasta">tabular to fasta</option>
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9 <option value="tabular2fastaweight">tabular to weighted fasta</option>
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10 <option value="fastaweight2fastaweight">recompile weighted fasta to catenated fasta weighted</option>
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11 <option value="fastaweight2fasta">fasta weighted to fasta</option>
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12 </param>
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13 <when value="fasta2tabular">
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14 <param name="input" type="data" format="fasta" label="fasta file to convert to tabular"/>
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15 </when>
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16 <when value="tabular2fasta">
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17 <param name="input" type="data" format="tabular" label="tabular file to convert to fasta"/>
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18 </when>
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19 <when value="tabular2fastaweight">
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20 <param name="input" type="data" format="tabular" label="tabular file to convert to fasta weighted"/>
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21 </when>
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22 <when value="fastaweight2fastaweight">
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23 <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"/>
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24 </when>
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25 <when value="fastaweight2fasta">
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26 <param name="input" type="data" format="fasta" label="fasta weighted file to convert to fasta"/>
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27 </when>
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28 </conditional>
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29
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30 </inputs>
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31
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32 <outputs>
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33 <data format="fasta" name="output" label="${switch.conversionType} conversion">
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34 <change_format>
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35 <when input="switch.conversionType" value="fasta2tabular" format="tabular"/>
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36 <when input="switch.conversionType" value="fastaweight2fastaweight" format="fasta"/>
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37 <when input="switch.conversionType" value="fastaweight2fasta" format="fasta"/>
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38 </change_format>
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39 </data>
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40 </outputs>
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41
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42 <tests>
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43 <test>
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44 <param name="conversionType" value="fasta2tabular" />
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45 <param ftype="fasta" name="input" value="input.fa" />
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46 <output file="output.tab" name="output" />
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47 </test>
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48 <test>
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49 <param name="conversionType" value="tabular2fastaweight" />
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50 <param ftype="tabular" name="input" value="output.tab" />
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51 <output file="output.faw" name="output" />
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52 </test>
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53 </tests>
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54
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55
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56 <help>
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57
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58 **What it does**
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59
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60 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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61
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62 This format is suitable for storage of sequence datasets in the data library, and will be used in the future.
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63
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64 Regeneration of the original fasta file from the tabular format is ensured by the same tool
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65
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66 This tool also handle a fasta "weigthed" format with headers as:
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67 >id_numberofreads
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68 ATGCATGACCAGATAGGAC
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69 etc...
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70
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71 with generation of the "weigthed" format from a tabular format, and recompilation of catenated weighted fasta files
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72
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73 </help>
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74
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75 </tool>