/tools/next_gen_conversion/fastq_conversions.xml
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1<tool id="fastq_conversions" name="FASTQ Conversions" version="1.0.0"> 2 <description>converts between FASTQ data and other data formats</description> 3 <command interpreter="python"> 4 fastq_conversions.py 5 --command=$conversionType.type 6 --input=$input 7 #if $conversionType.type == "sol2std": 8 --outputFastqsanger=$outputFastqsanger 9 #else: 10 --outputFastqsanger="None" 11 #end if 12 #if $conversionType.type == "std2sol": 13 --outputFastqsolexa=$outputFastqsolexa 14 #else: 15 --outputFastqsolexa="None" 16 #end if 17 #if $conversionType.type == "fq2fa": 18 --outputFasta=$outputFasta 19 #else: 20 --outputFasta="None" 21 #end if 22 </command> 23 <inputs> 24 <conditional name="conversionType"> 25 <param name="type" type="select" label="What type of conversion do you want to do?"> 26 <option value="sol2std">Solexa/Illumina FASTQ to standard Sanger FASTQ</option> 27 <option value="std2sol">Standard Sanger FASTQ to Solexa/Illumina FASTQ</option> 28 <option value="fq2fa">Various FASTQ to FASTA</option> 29 </param> 30 <when value="sol2std"> 31 <param name="input" type="data" format="fastqsolexa" label="File to convert" /> 32 </when> 33 <when value="std2sol"> 34 <param name="input" type="data" format="fastqsanger" label="File to convert" /> 35 </when> 36 <when value="fq2fa"> 37 <param name="input" type="data" format="fastqsolexa, fastqsanger" label="File to convert" /> 38 </when> 39 </conditional> 40 </inputs> 41 <outputs> 42 <data name="outputFastqsanger" format="fastqsanger"> 43 <filter>conversionType['type'] == 'sol2std'</filter> 44 </data> 45 <data name="outputFastqsolexa" format="fastqsolexa"> 46 <filter>conversionType['type'] == 'std2sol'</filter> 47 </data> 48 <data name="outputFasta" format="fasta"> 49 <filter>conversionType['type'] == 'fq2fa'</filter> 50 </data> 51 </outputs> 52 <tests> 53 <test> 54 <param name="type" value="sol2std" /> 55 <param name="input" value="fastq_conv_in1.fastq" ftype="fastqsolexa" /> 56 <output name="outputFastqsanger" file="fastq_conv_out1.fastqsanger" /> 57 </test> 58 <test> 59 <param name="type" value="std2sol" /> 60 <param name="input" value="1.fastqsanger" ftype="fastqsanger" /> 61 <output name="outputFastqsolexa" file="fastq_conv_out2.fastqsolexa" /> 62 </test> 63 <test> 64 <param name="type" value="fq2fa" /> 65 <param name="input" value="1.fastqsanger" ftype="fastqsanger" /> 66 <output name="outputFasta" file="fastq_conv_out4.fasta" /> 67 </test> 68 </tests> 69 <help> 70**What it does** 71 72This tool offers several conversions options relating to the FASTQ format. 73 74----- 75 76**Examples** 77 78- Converting the Solexa/Illumina FASTQ data:: 79 80 @081017-and-081020:1:1:1715:1759 81 GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC 82 + 83 II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B 84 85- will produce the following Sanger FASTQ data:: 86 87 @081017-and-081020:1:1:1715:1759 88 GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC 89 + 90 ++!+++++++!!!!!"+++++++!!!!)!%!!+!!%! 91 92- Converting standard Sanger FASTQ:: 93 94 @1831_573_1004/1 95 AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG 96 + 97 ><C&&9952+C>5<.?<79,=42<292:<(9/-7 98 @1831_573_1050/1 99 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT 100 + 101 ;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, 102 103- will produce the following Solexa/Illumina FASTQ data:: 104 105 @1831_573_1004/1 106 AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG 107 + 108 ][bEEXXTQJb]T[M^[VXK\SQ[QXQY[GXNLV 109 @1831_573_1050/1 110 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT 111 + 112 Z__PV^_\]V^^_`W^\\_S`^`SHEJMFEJFPK 113 114- Converting the Sanger FASTQ data:: 115 116 @1831_573_1004/1 117 AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG 118 + 119 ><C&&9952+C>5<.?<79,=42<292:<(9/-7 120 @1831_573_1050/1 121 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT 122 + 123 ;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, 124 125- will produce the following FASTA data:: 126 127 >1831_573_1004/1 128 AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG 129 >1831_573_1050/1 130 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT 131 132 </help> 133</tool>