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1 <tool id ="pyFastqSplitter" name="pyFastqSplitter" force_history_refresh="True">
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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 pyFastqSplitter.pl
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7 -f $f
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8 --o1 $out1
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9 --id $label.value
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10 --o2 $out2
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11 --file_type $ftype.type
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12 #if $joinc.ch == "-c":
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13 -c $joinc.c
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14 #end if#
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15 </command>
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16 <version_command>/usr/local/bin/pyFastqSplitter.py --version</version_command>
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17 <inputs>
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18 <conditional name="ftype">
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19 <param name="type" type="select" label="File type">
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20 <option value="fastq" selected="true">FASTQ</option>
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21 <option value="fasta">FASTA</option>
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22 </param>
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23 <when value="fastq">
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24 <param format="fastq" name="f" type="data" label="FastQ File -f" help="FastQ format" />
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25 </when>
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26 <when value="fasta">
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27 <param format="fasta" name="f" type="data" label="FastA File -f" help="FastA format" />
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28 </when>
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29 </conditional>
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30 <conditional name="joinc">
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31 <param name="ch" type="select" label="Insert a character at join">
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32 <option value="" selected="true">NO</option>
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33 <option value="-c">YES</option>
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34 </param>
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35 <when value="-c">
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36 <param type="text" name="c" label="Split the reads on the -c character" value=":" >
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37 <validator type="empty_field" message="enter a character or turn this option off" />
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38 </param>
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39 </when>
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40 <when value="">
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41 </when>
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42 </conditional>
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43 <param name="label" type="text" format="txt" size="30" value="pyFastqSplitter" label="Enter output file label -o" />
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44 </inputs>
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45 <outputs>
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46 <data format="input" name="out1" label="${label.value}_1.${ftype.type}"/>
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47 <data format="input" name="out2" label="${label.value}_2.${ftype.type}"/>
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48 <change_format>
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49 <when input="ftype.type" value="fasta" format="fasta" />
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50 </change_format>
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51 </outputs>
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52 <help>
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53
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54 .. class:: infomark
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55
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56 **pyFastqSplitter**
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57
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58 pyFastqSplitter is part of the pyCRAC_ package. Splits a merged fastq file (pyFastqJoiner output) in to two files.
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59
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60 Example::
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61
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62 Here the ":" character was used to separate the two sequences. By using the -c flag you can tell pyFastqSplitter where to split the sequences.
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63 This character is ignored by pyFastqDuplicateRemover
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64
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65
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66 @FCC102EACXX:3:1101:1343:2181#ATCACGAT/1##CAATAG@FCC102EACXX:3:1101:1343:2181#ATCACGAT/2
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67 CAAATTAGAGTGTTCAAAGCAGGCGTATTGCTCGAAT:AGCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCAAAGA
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68 +
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69 `efhYb][bdQQ`eeaeaYbeY^ceU__IXa[^ZYaeYJaSJ`Z`K`YbSb[[daeJRR[YeWd_I^I^ecgc]OV\bdeaegbXb
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70 @FCC102EACXX:3:1101:1424:2248#ATCACGAT/1##CCAGGA@FCC102EACXX:3:1101:1424:2248#ATCACGAT/2
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71 CTAACCATAAACTATGCCTACTAGGGATCCAGAGGTG:AAGTCCTTTAAGTTACAGCCTTGCGACCATACTACACCCAGAACCCAAA
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72 +
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73 ^_adddhJbaehbedd`dIb_^cXaRI^BBBBBBBBBYJJ\`JQY\`KJ`gY[[QRYY[[`H[_ceI^e[PYO^IWOHW^eaefhh
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74 @FCC102EACXX:3:1101:1623:2036#ATCACGAN/1##CTCAGC@FCC102EACXX:3:1101:1623:2036#ATCACGAN/2
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75 CAAAGTTAGGGGATCGAAGATGATCAGATACCGTCGT:GGCCAATCCTTATTGTGTCTGGACCTGGTGAGTTTCCCCGTGTTGAGTC
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76 +
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77 bghfc^YbgbeadggfdffeaS^ac_X^cegaGZ_efPP\`ccQ`eY[bQQ[d`ghehaghfgdg[`gb^bd[ePbH^c_c\a_eg
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78
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79 Result:
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80
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81 Forward reaction:
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82
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83 @FCC102EACXX:3:1101:1343:2181#ATCACGAT/1##CAATAG
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84 CAAATTAGAGTGTTCAAAGCAGGCGTATTGCTCGAAT
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85 +
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86 `efhYb][bdQQ`eeaeaYbeY^ceU__IXa[^ZYae
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87 @FCC102EACXX:3:1101:1424:2248#ATCACGAT/1##CCAGGA
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88 CTAACCATAAACTATGCCTACTAGGGATCCAGAGGTG
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89 +
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90 ^_adddhJbaehbedd`dIb_^cXaRI^BBBBBBBBB
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91 @FCC102EACXX:3:1101:1623:2036#ATCACGAN/1##CTCAGC
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92 CAAAGTTAGGGGATCGAAGATGATCAGATACCGTCGT
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93 +
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94 bghfc^YbgbeadggfdffeaS^ac_X^cegaGZ_ef
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95 @FCC102EACXX:3:1101:1574:2214#ATCACGAT/1##CGTTTT
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96 CTAATGACCCACTCGGCACCTTACGAAATCAAAGTCT
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97 +
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98 cdfgYY`cefhhZef\eaggXaceeghfQaeghWNW\
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99
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100 Reverse reaction:
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101
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102 @FCC102EACXX:3:1101:1343:2181#ATCACGAT/2
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103 AGCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCAAAGA
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104 +
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105 YJaSJ`Z`K`YbSb[[daeJRR[YeWd_I^I^ecgc]OV\bdeaegbXb
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106 @FCC102EACXX:3:1101:1424:2248#ATCACGAT/2
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107 AAGTCCTTTAAGTTACAGCCTTGCGACCATACTACACCCAGAACCCAAA
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108 +
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109 YJJ\`JQY\`KJ`gY[[QRYY[[`H[_ceI^e[PYO^IWOHW^eaefhh
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110 @FCC102EACXX:3:1101:1623:2036#ATCACGAN/2
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111 GGCCAATCCTTATTGTGTCTGGACCTGGTGAGTTTCCCCGTGTTGAGTC
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112 +
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113 PP\`ccQ`eY[bQQ[d`ghehaghfgdg[`gb^bd[ePbH^c_c\a_eg
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114
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115 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
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116
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117 ------
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118
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119 **Parameter list**
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120
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121 Options::
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122
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123 -f fastq_file, --filename=fastq_file
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124 To provide the names of two raw data files separated
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125 by a single space. Default = standard input
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126 --file_type=FASTQ
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127 Can split joined fasta and fastq files. Fastq is default
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128 If there isn't a specific character splitting the two reads
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129 the tool assumes that the two reads were of equal length
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130 -o splitfastq, --outfile=splitfastq
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131 Provide the name of the output files (WITHOUT file
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132 extension). By default the data will be printed to the
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133 standard output
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134 -c :, --character=:
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135 If the joined sequences were separated by a specific
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136 character then the program can divide the sequences by
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137 looking for that character
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138
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139 </help>
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140 </tool>
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