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1 <tool id="fa-extract-sequence" name="Fasta Extract Sequence" version="1.0.0">
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2 <description>Extract a single sequence from a fasta file.</description>
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3 <requirements>
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4 <requirement type="package" version="5.18.1">perl</requirement>
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5 <requirement type="package" version="1.6.924">bioperl</requirement>
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6 </requirements>
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7 <command interpreter="perl">
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8 fa-extract-few.pl
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9 -f $dataset
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10 $exact
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11 $inverse
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12 #if $file_or_type.select == "list"
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13 --list $file_or_type.list_file
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14 #else
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15 $file_or_type.id
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16 #end if
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17
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18 >
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19 $output
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20 </command>
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21 <inputs>
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22 <param name="dataset" type="data" format="fasta" label="fasta or multifasta file" help="fasta dataset to get statistics for."/>
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23 <param name="exact" type="boolean" truevalue="--exact" label="Exact matches only" help="Will only match exact matches for fasta id"/>
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24 <param name="inverse" type="boolean" truevalue="--inverse" label="Entries NOT matching" help="Will return the sequences not matching the given ids"/>
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25
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26 <conditional name="file_or_type">
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27 <param name="select" type="select" label="List file or single pattern">
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28 <option value="list">List file</option>
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29 <option value="single">Single Pattern</option>
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30 </param>
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31 <when value="list">
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32 <param name="list_file" type="data" format="txt" help="List of pattern to find." label="List file"/>
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33 </when>
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34 <when value="single">
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35 <param name="id" type="text" label="Sequence ID (or partial)" help="Name of the sequence to extract. Will also match partial names and return all matches." />
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36 </when>
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37 </conditional>
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38
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39
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40 </inputs>
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41 <outputs>
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42 <data name="output" format="fasta" label="${tool.name} on ${on_string}: Fasta"/>
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43 </outputs>
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44 <tests>
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45 <test>
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46 <output/>
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47 </test>
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48 </tests>
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49 <help>
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50 **Fasta Extract Sequence**
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51 Extracts a fasta sequence from a multfasta by id (exact or partial)
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52
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53 Latest author:
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54 Written by Philip Mabon - Public Health Agency of Canada
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55
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56 Original authors:
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57 Written by Torsten Seemann - Victorian Bioinformatics Consortium
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58
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59 Wrapped by Simon Gladman - Victorian Bioinformatics Consortium
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60
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61
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62 ------
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63
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64 Outputs in fasta format.
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65
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66 ------
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67
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68 Inputs:
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69
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70 Fasta dataset
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71
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72 Sequence id
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73 </help>
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74 <citations>
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75 </citations>
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76 </tool>
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