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Alternative barcode splitters that move selected results to the users history.
author Jim Johnson <jj@umn.edu>
date Tue, 19 Jul 2011 13:03:32 -0500
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1 <tool id="cshl_fastx_barcode_splitter" name="Barcode Splitter" force_history_refresh="True">
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2 <description></description>
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3 <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
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4 <command interpreter="python">fastx_barcode_splitter_galaxy_wrapper.py
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5 ## params for galaxy wrapper
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6 $output
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7 "$output.id"
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8 "$input.ext"
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9 "$__new_file_path__"
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10 --barcodes='$barcodes'
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11 $BARCODE $input "$input.name" "$output.extra_files_path"
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12 ## params for fastx_barcode_splitter
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13 --mismatches $mismatches --partial $partial $EOL
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14 </command>
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15
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16 <inputs>
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17 <param format="txt" name="BARCODE" type="data" label="Barcodes to use" />
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18 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />
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19
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20 <param name="EOL" type="select" label="Barcodes found at">
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21 <option value="--bol">Start of sequence (5' end)</option>
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22 <option value="--eol">End of sequence (3' end)</option>
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23 </param>
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24
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25 <param name="mismatches" type="integer" size="3" value="2" label="Number of allowed mismatches" />
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26
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27 <param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
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28
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29 <param name="barcodes" type="select" multiple="true" label="Select barcodes to add as new datasets to history">
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30 <options from_dataset="BARCODE">
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31 <column name="name" index="0"/>
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32 <column name="value" index="0"/>
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33 <filter type="unique_value" name="unq_bc" column="0" />
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34 <filter type="add_value" name="unmatched" value="unmatched"/>
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35 </options>
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36 </param>
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37 </inputs>
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38
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39 <outputs>
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40 <data format="html" name="output" />
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41 </outputs>
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42
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43 <tests>
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44 <test>
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45 <!-- Split a FASTQ file -->
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46 <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
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47 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
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48 <param name="EOL" value="Start of sequence (5' end)" />
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49 <param name="mismatches" value="2" />
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50 <param name="partial" value="0" />
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51 <output name="output" file="fastx_barcode_splitter1.out" />
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52 </test>
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53 </tests>
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54
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55 <help>
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56
bc23f6946bb8 Alternative barcode splitters that move selected results to the users history.
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57 **What it does**
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58
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59 This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria.
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60
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61 --------
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62
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63 **Barcode file Format**
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64
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65 Barcode files are simple text files.
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66 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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67 Example::
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68
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69 #This line is a comment (starts with a 'number' sign)
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70 BC1 GATCT
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71 BC2 ATCGT
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72 BC3 GTGAT
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73 BC4 TGTCT
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74
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75 For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name).
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76 Sequences matching the barcode will be stored in the appropriate file.
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77
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78 One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored.
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79
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80 The output of this tool is an HTML file, displaying the split counts and the file locations.
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81
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82 **Output Example**
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83
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84 .. image:: ./static/fastx_icons/barcode_splitter_output_example.png
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85
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86 </help>
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87 </tool>
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88 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->