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annotate fastx_barcode_splitter.xml @ 0:84bbf4fd24c3 draft

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Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history.
author lparsons
date Fri, 08 Nov 2013 09:53:39 -0500
parents
children b7b3d008e2d3
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1 <tool id="cshl_princeton_fastx_barcode_splitter" version="1.1" name="Barcode Splitter" force_history_refresh="True">
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2 <description></description>
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3 <command interpreter="bash">
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4 fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "primary_$output.id" "$__new_file_path__" $input.extension --mismatches $mismatches --partial $partial
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5 #if $refBarcodeLocation.barcodeLocation == "idxfile":
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6 --idxfile $refBarcodeLocation.idxfile
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7 #else:
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8 $refBarcodeLocation.EOL
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9 #end if
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10 > $output
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11 </command>
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12
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13 <inputs>
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14 <param format="txt" version="1.1" name="BARCODE" type="data" label="Barcodes to use" />
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15 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" version="1.1" name="input" type="data" label="Library to split" />
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16
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17 <conditional name="refBarcodeLocation">
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18 <param version="1.1" name="barcodeLocation" type="select" label="Barcodes found at">
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19 <option value="bol">Start of sequence (5' end)</option>
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20 <option value="eol">End of sequence (3' end)</option>
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21 <option value="idxfile">Separate index file</option>
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22 </param>
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23 <when value="bol">
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24 <param version="1.1" name="EOL" type="hidden" value="--bol" />
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25 </when>
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26 <when value="eol">
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27 <param version="1.1" name="EOL" type="hidden" value="--eol" />
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28 </when>
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29 <when value="idxfile">
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30 <param version="1.1" name="idxfile" type="data" format="fasta,fastq,fastqsanger" label="Select index read file" />
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31 </when>
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32 </conditional>
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33
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34 <param version="1.1" name="mismatches" type="integer" size="3" value="0" label="Number of allowed mismatches" />
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35
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36 <param version="1.1" name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
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37
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38 </inputs>
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39
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40 <tests>
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41 <test>
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42 <!-- Split a FASTQ file -->
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43 <param version="1.1" name="BARCODE" value="fastx_barcode_splitter1.txt" />
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44 <param version="1.1" name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
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45 <param version="1.1" name="EOL" value="Start of sequence (5' end)" />
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46 <param version="1.1" name="mismatches" value="2" />
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47 <param version="1.1" name="partial" value="0" />
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48 <output version="1.1" name="output" file="fastx_barcode_splitter1.out" />
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49 </test>
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50 </tests>
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51
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52 <outputs>
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53 <data version="1.1" format="html" name="output" />
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54 </outputs>
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55 <help>
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56
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57 **What it does**
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58
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59 This tool splits a FASTQ or 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 names.
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81 In addition, each fastq file produced will be loaded into the galaxy history automatically.
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82
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83
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84 ------
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85
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86 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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87
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88 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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89
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90 </help>
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91 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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92 </tool>