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1 <tool id ="pyFastqJoiner" name="pyFastqJoiner">
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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="python">
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6 /usr/local/bin/pyFastqJoiner.py
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7 -f $ftype.f1 $ftype.f2
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8 -o $out
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9 --file_type=$ftype.type
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10 #if $joinc.ch == "-c":
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11 -c $joinc.c
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12 #end if#
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13 </command>
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14 <version_command>/usr/local/bin/pyFastqJoiner.py --version</version_command>
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15 <inputs>
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16 <conditional name="ftype">
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17 <param name="type" type="select" label="File type">
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18 <option value="fastq" selected="true">FASTQ</option>
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19 <option value="fasta">FASTA</option>
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20 </param>
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21 <when value="fastq">
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22 <param format="fastq" name="f1" type="data" label="First FastQ File -f" help="FastQ format" />
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23 <param format="fastq" name="f2" type="data" label="Second FastQ File -f" help="FastQ format" />
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24 </when>
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25 <when value="fasta">
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26 <param format="fasta" name="f1" type="data" label="First FastA File -f" help="FastA format" />
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27 <param format="fasta" name="f2" type="data" label="Second 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="Add this character -c" 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="pyFastqJoiner" 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="out" label="${label.value}.${ftype.type}"/>
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47 <change_format>
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48 <when input="ftype.type" value="fasta" format="fasta" />
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49 </change_format>
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50 </outputs>
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51 <help>
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52
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53 .. class:: infomark
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54
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55 **pyFastqJoiner**
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56
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57 pyFastqJoiner is part of the pyCRAC_ package. Merges paired sequences from two fastq or fasta formatted files.
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58
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59 Example::
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60
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61 Forward reaction:
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62
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63 @FCC102EACXX:3:1101:1343:2181#ATCACGAT/1##CAATAG
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64 CAAATTAGAGTGTTCAAAGCAGGCGTATTGCTCGAAT
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65 +
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66 `efhYb][bdQQ`eeaeaYbeY^ceU__IXa[^ZYae
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67 @FCC102EACXX:3:1101:1424:2248#ATCACGAT/1##CCAGGA
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68 CTAACCATAAACTATGCCTACTAGGGATCCAGAGGTG
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69 +
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70 ^_adddhJbaehbedd`dIb_^cXaRI^BBBBBBBBB
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71 @FCC102EACXX:3:1101:1623:2036#ATCACGAN/1##CTCAGC
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72 CAAAGTTAGGGGATCGAAGATGATCAGATACCGTCGT
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73 +
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74 bghfc^YbgbeadggfdffeaS^ac_X^cegaGZ_ef
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75 @FCC102EACXX:3:1101:1574:2214#ATCACGAT/1##CGTTTT
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76 CTAATGACCCACTCGGCACCTTACGAAATCAAAGTCT
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77 +
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78 cdfgYY`cefhhZef\eaggXaceeghfQaeghWNW\
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79
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80 Reverse reaction:
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81
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82 @FCC102EACXX:3:1101:1343:2181#ATCACGAT/2
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83 AGCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCAAAGA
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84 +
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85 YJaSJ`Z`K`YbSb[[daeJRR[YeWd_I^I^ecgc]OV\bdeaegbXb
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86 @FCC102EACXX:3:1101:1424:2248#ATCACGAT/2
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87 AAGTCCTTTAAGTTACAGCCTTGCGACCATACTACACCCAGAACCCAAA
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88 +
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89 YJJ\`JQY\`KJ`gY[[QRYY[[`H[_ceI^e[PYO^IWOHW^eaefhh
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90 @FCC102EACXX:3:1101:1623:2036#ATCACGAN/2
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91 GGCCAATCCTTATTGTGTCTGGACCTGGTGAGTTTCCCCGTGTTGAGTC
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92 +
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93 PP\`ccQ`eY[bQQ[d`ghehaghfgdg[`gb^bd[ePbH^c_c\a_eg
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94
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95 Here the ":" character is used to split the two sequences. This character tells pyFastqSplitter where to split the sequences.
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96 This character is ignored by pyFastqDuplicateRemover
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97
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98 Result:
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99
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100 @FCC102EACXX:3:1101:1343:2181#ATCACGAT/1##CAATAG@FCC102EACXX:3:1101:1343:2181#ATCACGAT/2
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101 CAAATTAGAGTGTTCAAAGCAGGCGTATTGCTCGAAT:AGCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCAAAGA
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102 +
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103 `efhYb][bdQQ`eeaeaYbeY^ceU__IXa[^ZYaeYJaSJ`Z`K`YbSb[[daeJRR[YeWd_I^I^ecgc]OV\bdeaegbXb
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104 @FCC102EACXX:3:1101:1424:2248#ATCACGAT/1##CCAGGA@FCC102EACXX:3:1101:1424:2248#ATCACGAT/2
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105 CTAACCATAAACTATGCCTACTAGGGATCCAGAGGTG:AAGTCCTTTAAGTTACAGCCTTGCGACCATACTACACCCAGAACCCAAA
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106 +
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107 ^_adddhJbaehbedd`dIb_^cXaRI^BBBBBBBBBYJJ\`JQY\`KJ`gY[[QRYY[[`H[_ceI^e[PYO^IWOHW^eaefhh
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108 @FCC102EACXX:3:1101:1623:2036#ATCACGAN/1##CTCAGC@FCC102EACXX:3:1101:1623:2036#ATCACGAN/2
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109 CAAAGTTAGGGGATCGAAGATGATCAGATACCGTCGT:GGCCAATCCTTATTGTGTCTGGACCTGGTGAGTTTCCCCGTGTTGAGTC
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110 +
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111 bghfc^YbgbeadggfdffeaS^ac_X^cegaGZ_efPP\`ccQ`eY[bQQ[d`ghehaghfgdg[`gb^bd[ePbH^c_c\a_eg
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112
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113 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
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114
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115 ------
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116
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117 **Parameter list**
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118
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119 Options::
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120
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121 -f fastq_file1 fastq_file2
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122 Provide the names of two raw data files separated by a single space.
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123 Make sure the first file is the data file of the forward (/1) sequencing reaction.
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124
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125 --file_type=FASTQ
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126 Can join fasta and fastq files. Fastq is default
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127
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128 -o mergedfastq.fastq, --outfile=mergedfastq.fastq
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129 provide the name of the output file. By default it
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130 will be printed to the standard output
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131
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132 -c :
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133 This option adds the '|' character between the DNA
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134 sequences so that it is much easier to split the data
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135 again later on
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136
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137
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138 </help>
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139 </tool>
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