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1 <tool id="ngs-tools_split_by_barcode" name="Barcode Splitter (ngs-tools)" force_history_refresh="True">
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2 <description></description>
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3
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3 <requirements>
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4 <requirement type="package" version="0.1.4">ngs-tools</requirement>
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5 </requirements>
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6 <command>
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7 ngs-tools split-by-barcode
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8 $trim_barcode $input_format.format
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9 --barcode-size $barcode_length --max-distance $max_distance
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10 #for $i in $barcodes
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11 --barcode ${i.barcode}
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12 #end for
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13 --report $output1 --galaxy $output1.id --output $__new_file_path__
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14 $barcode_index
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15 #for $i in $input_format.inputs
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16 ${i.input}
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17 #end for
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18 </command>
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19
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20 <inputs>
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21 <conditional name="input_format">
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22 <param name="format" type="select" label="Input format">
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23 <option value="--fastq" selected="true">Fastq</option>
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24 <option value="">Fasta</option>
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25 </param>
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26 <when value="--fastq">
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27 <repeat name="inputs" title="Dataset" help="Datasets to split.">
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28 <param name="input" type="data" label="Dataset to split" format="fastq,fastqsanger,fastqsolexa,fastqillumina" />
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29 </repeat>
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30 </when>
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31 <when value="">
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32 <repeat name="inputs" title="Dataset" help="Datasets to split.">
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33 <param name="input" type="data" label="Dataset to split" format="fasta" />
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34 </repeat>
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35 </when>
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36 </conditional>
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37 <param format="tabular" name="barcode_index" type="data" label="Barcodes index" help="See below for description." />
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38 <param name="barcode_length" type="integer" size="3" value="11" label="Barcode length" help="Please specify the barcode length." />
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39 <repeat name="barcodes" title="Barcode" help="Barcodes to use. By default all barcodes with the correct length in the index are used. By using this option you can limit which ones to use.">
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40 <param name="barcode" type="text" label="Barcode to use" />
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41 </repeat>
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42 <param name="trim_barcode" type="select" label="Trim the barcode" help="By default barcodes are trimmed from the resulting splitted datasets">
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43 <option value="" selected="true">Yes</option>
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44 <option value="--keep-barcode">No</option>
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45 </param>
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46 <param name="max_distance" type="integer" size="3" value="2" label="Number of allowed polymorphisms" help="Max Levenshtein's distance when looking for mutated barcodes." />
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47 </inputs>
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48
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49 <outputs>
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50 <data format="interval" name="output1" />
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51 </outputs>
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52 <help>
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53
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54 **What it does**
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55
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56 This tool splits FASTQ or FASTA datasets into several datasets, using barcodes as the split criteria.
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57
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58 --------
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59
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60 **Barcode index format**
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61
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62 Barcode index datasets are simple tab separated files.
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63 Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character.
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64 Example::
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65
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66 RL001 ACACGACGACT
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67 RL002 ACACGTAGTAT
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68 RL003 ACACTACTCGT
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69 RL004 ACGACACGTAT
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70 RL005 ACGAGTAGACT
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71
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72 For each barcode, a new FASTQ or FASTA dataset will be created (with the barcode's identifier as part of the dataset name).
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73 Sequences matching the barcode will be stored in the appropriate dataset.
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74
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75 One additional FASTQ or FASTA dataset will be created (the 'Unassigned' dataset), where sequences not matching any barcode will be stored.
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76
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77 The output of this tool is one history dataset per each barcode provided plus a report with the split counts.
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78
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79 ------
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80
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81 This tool is based on `ngs-tools`__ by Carlos Borroto <carlos.borroto@gmail.com>.
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82
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83 .. __: https://github.com/cjav/ngs-tools/
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84
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85 </help>
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86 </tool>
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