Mercurial > repos > lparsons > fastx_barcode_splitter_enhanced

annotate fastx_barcode_splitter.xml @ 3:e7b7cdc1834d draft

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit a3b5b09c69f880529df96bdd5e050d712fa35cf4-dirty
author lparsons
date Fri, 11 Mar 2016 17:24:31 -0500
parents 32304398ef67
children 0fb7e9130a70
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1 <tool id="cshl_princeton_fastx_barcode_splitter" version="1.1" name="Barcode Splitter">
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2 <description></description>
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3 <command interpreter="bash"><![CDATA[
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4 fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "split/" $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 ]]>
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12 </command>
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14 <inputs>
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15 <param format="txt" name="BARCODE" type="data" label="Barcodes to use" />
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16 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />
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18 <conditional name="refBarcodeLocation">
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19 <param name="barcodeLocation" type="select" label="Barcodes found at">
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20 <option value="bol">Start of sequence (5' end)</option>
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21 <option value="eol">End of sequence (3' end)</option>
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22 <option value="idxfile">Separate index file</option>
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23 </param>
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24 <when value="bol">
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25 <param name="EOL" type="hidden" value="--bol" />
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26 </when>
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27 <when value="eol">
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28 <param name="EOL" type="hidden" value="--eol" />
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29 </when>
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30 <when value="idxfile">
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31 <param name="idxfile" type="data" format="fasta,fastq,fastqsanger" label="Select index read file" />
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32 </when>
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33 </conditional>
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34
1
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35 <param name="mismatches" type="integer" size="3" value="0" label="Number of allowed mismatches" />
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37 <param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
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38
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39 </inputs>
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41 <outputs>
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42 <data format="html" name="output">
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43 <discover_datasets pattern="__designation_and_ext__" directory="split" visible="true" label="${tool.name}: ${designation}"/>
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44 </data>
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45 </outputs>
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47 <tests>
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48 <test>
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49 <!-- Split a FASTQ file -->
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50 <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
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51 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
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52 <param name="barcodeLocation" value="bol" />
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53 <param name="mismatches" value="2" />
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54 <param name="partial" value="0" />
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55 <output name="output" file="fastx_barcode_splitter1.out">
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56 <discovered_dataset designation="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
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57 <discovered_dataset designation="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
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58 <discovered_dataset designation="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
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59 <discovered_dataset designation="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
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60 <discovered_dataset designation="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
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61 </output>
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62 </test>
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63 <test>
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64 <!-- Split a FASTQ file, using separate index read -->
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65 <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
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66 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
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67 <param name="idxfile" value="fastx_barcode_splitter_index.fastq" ftype="fastqsolexa" />
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68 <param name="barcodeLocation" value="idxfile" />
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69 <param name="mismatches" value="2" />
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70 <param name="partial" value="0" />
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71 <output name="output" file="fastx_barcode_splitter1.out">
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72 <discovered_dataset designation="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
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73 <discovered_dataset designation="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
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74 <discovered_dataset designation="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
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75 <discovered_dataset designation="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
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76 <discovered_dataset designation="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
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77 </output>
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78 </test>
0
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79 </tests>
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80
1
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81 <help><![CDATA[
0
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82 **What it does**
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83
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84 This tool splits a FASTQ or FASTA file into several files, using barcodes as the split criteria.
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85
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86 --------
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87
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88 **Barcode file Format**
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89
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90 Barcode files are simple text files.
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91 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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92 Example::
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93
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94 #This line is a comment (starts with a 'number' sign)
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95 BC1 GATCT
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96 BC2 ATCGT
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97 BC3 GTGAT
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98 BC4 TGTCT
1
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99
0
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100 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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101 Sequences matching the barcode will be stored in the appropriate file.
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102
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103 One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored.
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104
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105 The output of this tool is an HTML file, displaying the split counts and the file names.
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106 In addition, each fastq file produced will be loaded into the galaxy history automatically.
1
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107 ]]>
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108 </help>
0
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109
1
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110 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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111 <citations>
2
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112 <citation type="bibtex">
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113 @misc{gordon_fastx-toolkit_????,
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114 title = {{FASTX}-{Toolkit}},
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115 url = {http://hannonlab.cshl.edu/fastx_toolkit/index.html},
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116 author = {Gordon, Assaf}
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117 }
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118 </citation>
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119 </citations>
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120
0
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121 </tool>