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1 <tool id ="pyFastqDuplicateRemover" name="pyFastqDuplicateRemover">
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2 <requirements>
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3 <requirement type="package">pyCRAC</requirement>
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4 </requirements>
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5 <command interpreter="perl">
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6 pyFastqDuplicateRemover.pl
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7 -f $ftype.f
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8 #if $ftype.reverse.rev == "yes":
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9 -r=$ftype.reverse.r
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10 --out2 $out2
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11 #end if#
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12 -o $out
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13 --id $out.id
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14 </command>
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15 <version_command>pyFastqDuplicateRemover.py --version</version_command>
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16 <inputs>
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17 <conditional name="ftype">
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18 <param name="type" type="select" label="File type">
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19 <option value="fastq" selected="true">FASTQ</option>
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20 <option value="fasta">FASTA</option>
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21 </param>
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22 <when value="fastq">
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23 <param format="fastq" name="f" type="data" label="FastQ File -f" help="FastQ format" />
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24 <conditional name="reverse">
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25 <param name="rev" type="select" label="Add a reverse or paired FastQ file">
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26 <option value="no" selected="true">NO</option>
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27 <option value="yes">YES</option>
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28 </param>
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29 <when value="yes">
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30 <param format="fastq" name="r" type="data" label="Reverse FastQ File -f" help="FastQ format" />
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31 </when>
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32 <when value="no">
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33 </when>
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34 </conditional>
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35 </when>
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36 <when value="fasta">
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37 <param format="fasta" name="f" type="data" label="FastA File -f" help="FastA format" />
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38 <conditional name="reverse">
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39 <param name="rev" type="select" label="Add a reverse or paired FastA file">
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40 <option value="no" selected="true">NO</option>
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41 <option value="yes">YES</option>
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42 </param>
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43 <when value="yes">
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44 <param format="fasta" name="r" type="data" label="Reverse FastA File -f" help="FastA format" />
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45 </when>
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46 <when value="no">
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47 </when>
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48 </conditional>
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49 </when>
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50 </conditional>
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51 <param name="label" type="text" format="txt" size="30" value="pyFastqDuplicateRemover" label="Enter output file label -o" />
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52 </inputs>
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53 <outputs>
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54 <data format="fasta" name="out" label="${label.value}.fasta"/>
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55 <data format="fasta" name="out2" label="${label.value}_reverse.fasta">
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56 <filter>ftype['reverse']['rev'] == "yes"</filter>
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57 </data>
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58 </outputs>
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59 <help>
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60
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61 .. class:: infomark
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62
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63 **pyFastqDuplicateRemover**
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64
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65 pyFastqDuplicateRemover is part of the pyCRAC_ package. Removes identical sequences from fastq and fasta files and returns a fasta file with collapsed data.
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66
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67 Can also process paired-end data.
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68
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69 **Examples**
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70
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71 Unprocessed fastq data with six random nucleotides at 5' end of the read::
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72
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73 @FCC102EACXX:3:1101:3231:2110#TGACCAAT/1
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74 GCGCCTGCCAATTCCATCGTAATGATTAATAGGGACGGTCGGGGGCATC
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75 +
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76 bb_ceeeegggggiiiiiifghiihiihiiiiiiiiiifggfhiecccc
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77
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78 After pyBarcodeFilter::
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79
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80 @FCC102EACXX:3:1101:3231:2110#TGACCAAT/1##GCGCCT
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81 TCCATCGTAATGATTAATAGGGACGGTCGGGGGCATC
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82 +
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83 giiiiiifghiihiihiiiiiiiiiifggfhiecccc
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84
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85 This entry is printed to the NNNNNNGCCAAT barcode file.
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86
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87 After pyFastqDuplicateRemover::
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88
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89 >1_GCGCCT_5/1
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90 TCCATCGTAATGATTAATAGGGACGGTCGGGGGCATC
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91
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92 The '1' indicates that this is the first unique cDNA in the data
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93 GCGCCT is the random barcode sequence
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94 the '5' indicates that 5 reads were found with identical read and random barcode sequences
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95 the '/1' indicates that the seqeuence originates from the forward sequencing reaction
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96
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97 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
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98
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99 ------
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100
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101 **Parameter list**
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102
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103 Options::
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104
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105 -f FILE, --input_file=FILE
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106 name of the FASTQ or FASTA input file
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107
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108 -r FILE, --reverse_input_file=FILE
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109 name of the paired (or reverse) FASTQ or FASTA input file
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110
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111 -o FILE, --output_file=FILE
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112 Provide the path and name of the fastq or fasta output file. Default is standard output.
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113 For paired-end data just provide a file name without file extension (!)
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114 </help>
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115 </tool>
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116
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117
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