annotate tools/next_gen_conversion/fastq_conversions.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="fastq_conversions" name="FASTQ Conversions" version="1.0.0">
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2 <description>converts between FASTQ data and other data formats</description>
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3 <command interpreter="python">
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4 fastq_conversions.py
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5 --command=$conversionType.type
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6 --input=$input
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7 #if $conversionType.type == "sol2std":
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8 --outputFastqsanger=$outputFastqsanger
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9 #else:
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10 --outputFastqsanger="None"
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11 #end if
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12 #if $conversionType.type == "std2sol":
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13 --outputFastqsolexa=$outputFastqsolexa
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14 #else:
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15 --outputFastqsolexa="None"
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16 #end if
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17 #if $conversionType.type == "fq2fa":
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18 --outputFasta=$outputFasta
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19 #else:
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20 --outputFasta="None"
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21 #end if
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22 </command>
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23 <inputs>
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24 <conditional name="conversionType">
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25 <param name="type" type="select" label="What type of conversion do you want to do?">
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26 <option value="sol2std">Solexa/Illumina FASTQ to standard Sanger FASTQ</option>
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27 <option value="std2sol">Standard Sanger FASTQ to Solexa/Illumina FASTQ</option>
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28 <option value="fq2fa">Various FASTQ to FASTA</option>
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29 </param>
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30 <when value="sol2std">
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31 <param name="input" type="data" format="fastqsolexa" label="File to convert" />
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32 </when>
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33 <when value="std2sol">
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34 <param name="input" type="data" format="fastqsanger" label="File to convert" />
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35 </when>
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36 <when value="fq2fa">
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37 <param name="input" type="data" format="fastqsolexa, fastqsanger" label="File to convert" />
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38 </when>
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39 </conditional>
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40 </inputs>
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41 <outputs>
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42 <data name="outputFastqsanger" format="fastqsanger">
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43 <filter>conversionType['type'] == 'sol2std'</filter>
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44 </data>
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45 <data name="outputFastqsolexa" format="fastqsolexa">
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46 <filter>conversionType['type'] == 'std2sol'</filter>
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47 </data>
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48 <data name="outputFasta" format="fasta">
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49 <filter>conversionType['type'] == 'fq2fa'</filter>
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50 </data>
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="type" value="sol2std" />
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55 <param name="input" value="fastq_conv_in1.fastq" ftype="fastqsolexa" />
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56 <output name="outputFastqsanger" file="fastq_conv_out1.fastqsanger" />
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57 </test>
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58 <test>
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59 <param name="type" value="std2sol" />
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60 <param name="input" value="1.fastqsanger" ftype="fastqsanger" />
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61 <output name="outputFastqsolexa" file="fastq_conv_out2.fastqsolexa" />
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62 </test>
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63 <test>
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64 <param name="type" value="fq2fa" />
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65 <param name="input" value="1.fastqsanger" ftype="fastqsanger" />
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66 <output name="outputFasta" file="fastq_conv_out4.fasta" />
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67 </test>
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68 </tests>
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69 <help>
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70 **What it does**
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71
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72 This tool offers several conversions options relating to the FASTQ format.
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73
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74 -----
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75
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76 **Examples**
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77
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78 - Converting the Solexa/Illumina FASTQ data::
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79
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80 @081017-and-081020:1:1:1715:1759
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81 GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
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82 +
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83 II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&amp;&amp;B
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84
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85 - will produce the following Sanger FASTQ data::
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86
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87 @081017-and-081020:1:1:1715:1759
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88 GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
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89 +
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90 ++!+++++++!!!!!"+++++++!!!!)!%!!+!!%!
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91
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92 - Converting standard Sanger FASTQ::
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93
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94 @1831_573_1004/1
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95 AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
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96 +
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97 >&lt;C&amp;&amp;9952+C>5&lt;.?&lt;79,=42&lt;292:&lt;(9/-7
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98 @1831_573_1050/1
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99 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
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100 +
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101 ;@@17?@=>7??@A8?==@4A?A4)&amp;+.'&amp;+'1,
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102
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103 - will produce the following Solexa/Illumina FASTQ data::
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104
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105 @1831_573_1004/1
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106 AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
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107 +
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108 ][bEEXXTQJb]T[M^[VXK\SQ[QXQY[GXNLV
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109 @1831_573_1050/1
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110 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
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111 +
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112 Z__PV^_\]V^^_`W^\\_S`^`SHEJMFEJFPK
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113
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114 - Converting the Sanger FASTQ data::
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115
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116 @1831_573_1004/1
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117 AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
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118 +
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119 >&lt;C&amp;&amp;9952+C>5&lt;.?&lt;79,=42&lt;292:&lt;(9/-7
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120 @1831_573_1050/1
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121 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
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122 +
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123 ;@@17?@=>7??@A8?==@4A?A4)&amp;+.'&amp;+'1,
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124
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125 - will produce the following FASTA data::
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126
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127 >1831_573_1004/1
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128 AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
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129 >1831_573_1050/1
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130 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
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131
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132 </help>
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133 </tool>