annotate tools/fastq/fastq_groomer.xml @ 2:c2a356708570

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author xuebing
date Fri, 09 Mar 2012 19:45:42 -0500
parents 9071e359b9a3
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1 <tool id="fastq_groomer" name="FASTQ Groomer" version="1.0.4">
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2 <description>convert between various FASTQ quality formats</description>
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3 <command interpreter="python">fastq_groomer.py '$input_file' '$input_type' '$output_file'
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4 #if str( $options_type['options_type_selector'] ) == 'basic':
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5 #if str( $input_type ) == 'cssanger':
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6 'cssanger'
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7 #else:
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8 'sanger'
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9 #end if
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10 'ascii' 'summarize_input'
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11 #else:
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12 '${options_type.output_type}' '${options_type.force_quality_encoding}' '${options_type.summarize_input}'
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13 #end if
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14 </command>
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15 <inputs>
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16 <param name="input_file" type="data" format="fastq" label="File to groom" />
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17 <param name="input_type" type="select" label="Input FASTQ quality scores type">
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18 <option value="solexa">Solexa</option>
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19 <option value="illumina">Illumina 1.3+</option>
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20 <option value="sanger" selected="True">Sanger</option>
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21 <option value="cssanger">Color Space Sanger</option>
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22 </param>
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23 <conditional name="options_type">
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24 <param name="options_type_selector" type="select" label="Advanced Options">
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25 <option value="basic" selected="True">Hide Advanced Options</option>
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26 <option value="advanced">Show Advanced Options</option>
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27 </param>
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28 <when value="basic">
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29 <!-- no options -->
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30 </when>
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31 <when value="advanced">
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32 <param name="output_type" type="select" label="Output FASTQ quality scores type" help="Galaxy tools are designed to work with the Sanger Quality score format.">
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33 <option value="solexa">Solexa</option>
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34 <option value="illumina">Illumina 1.3+</option>
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35 <option value="sanger" selected="True">Sanger (recommended)</option>
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36 <option value="cssanger">Color Space Sanger</option>
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37 </param>
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38 <param name="force_quality_encoding" type="select" label="Force Quality Score encoding">
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39 <option value="None">Use Source Encoding</option>
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40 <option value="ascii" selected="True">ASCII</option>
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41 <option value="decimal">Decimal</option>
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42 </param>
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43 <param name="summarize_input" type="select" label="Summarize input data">
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44 <option value="summarize_input" selected="True">Summarize Input</option>
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45 <option value="dont_summarize_input">Do not Summarize Input (faster)</option>
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46 </param>
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47 </when>
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48 </conditional>
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49 </inputs>
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50 <outputs>
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51 <data name="output_file" format="fastqsanger">
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52 <change_format>
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53 <when input="input_type" value="cssanger" format="fastqcssanger" />
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54 <when input="options_type.output_type" value="solexa" format="fastqsolexa" />
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55 <when input="options_type.output_type" value="illumina" format="fastqillumina" />
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56 <when input="options_type.output_type" value="sanger" format="fastqsanger" />
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57 <when input="options_type.output_type" value="cssanger" format="fastqcssanger" />
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58 </change_format>
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59 </data>
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60 </outputs>
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61 <tests>
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62 <!-- These tests include test files adapted from supplemental material in Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16. -->
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63 <!-- Unfortunately, cannot test for expected failures -->
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64 <!-- Test basic options -->
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65 <test>
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66 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
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67 <param name="input_type" value="sanger" />
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68 <param name="options_type_selector" value="basic" />
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69 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
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70 </test>
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71 <test>
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72 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
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73 <param name="input_type" value="cssanger" />
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74 <param name="options_type_selector" value="basic" />
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75 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
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76 </test>
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77 <test>
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78 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
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79 <param name="input_type" value="illumina" />
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80 <param name="options_type_selector" value="basic" />
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81 <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" />
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82 </test>
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83 <test>
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84 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
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85 <param name="input_type" value="solexa" />
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86 <param name="options_type_selector" value="basic" />
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87 <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" />
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88 </test>
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89 <test>
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90 <param name="input_file" value="sanger_full_range_as_illumina.fastqillumina" ftype="fastq" />
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91 <param name="input_type" value="sanger" />
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92 <param name="options_type_selector" value="basic" />
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93 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
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94 </test>
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95 <!-- Test grooming from illumina -->
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96 <test>
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97 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
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98 <param name="input_type" value="illumina" />
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99 <param name="options_type_selector" value="advanced" />
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100 <param name="output_type" value="illumina" />
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101 <param name="force_quality_encoding" value="None" />
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102 <param name="summarize_input" value="summarize_input" />
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103 <output name="output_file" file="illumina_full_range_original_illumina.fastqillumina" />
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104 </test>
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105 <test>
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106 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
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107 <param name="input_type" value="illumina" />
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108 <param name="options_type_selector" value="advanced" />
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109 <param name="output_type" value="sanger" />
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110 <param name="force_quality_encoding" value="None" />
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111 <param name="summarize_input" value="summarize_input" />
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112 <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" />
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113 </test>
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114 <test>
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115 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
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116 <param name="input_type" value="illumina" />
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117 <param name="options_type_selector" value="advanced" />
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118 <param name="output_type" value="solexa" />
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119 <param name="force_quality_encoding" value="None" />
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120 <param name="summarize_input" value="summarize_input" />
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121 <output name="output_file" file="illumina_full_range_as_solexa.fastqsolexa" />
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122 </test>
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123 <test>
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124 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
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125 <param name="input_type" value="illumina" />
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126 <param name="options_type_selector" value="advanced" />
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127 <param name="output_type" value="cssanger" />
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128 <param name="force_quality_encoding" value="None" />
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129 <param name="summarize_input" value="summarize_input" />
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130 <output name="output_file" file="illumina_full_range_as_cssanger.fastqcssanger" />
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131 </test>
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132 <!-- Test grooming from sanger -->
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133 <test>
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134 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
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135 <param name="input_type" value="sanger" />
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136 <param name="options_type_selector" value="advanced" />
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137 <param name="output_type" value="sanger" />
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138 <param name="force_quality_encoding" value="None" />
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139 <param name="summarize_input" value="summarize_input" />
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140 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
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141 </test>
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142 <test>
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143 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
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144 <param name="input_type" value="sanger" />
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145 <param name="options_type_selector" value="advanced" />
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146 <param name="output_type" value="illumina" />
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147 <param name="force_quality_encoding" value="None" />
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148 <param name="summarize_input" value="summarize_input" />
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149 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
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150 </test>
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151 <test>
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152 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
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153 <param name="input_type" value="sanger" />
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154 <param name="options_type_selector" value="advanced" />
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155 <param name="output_type" value="solexa" />
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156 <param name="force_quality_encoding" value="None" />
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157 <param name="summarize_input" value="summarize_input" />
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158 <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" />
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159 </test>
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160 <test>
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161 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
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162 <param name="input_type" value="sanger" />
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163 <param name="options_type_selector" value="advanced" />
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164 <param name="output_type" value="cssanger" />
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165 <param name="force_quality_encoding" value="None" />
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166 <param name="summarize_input" value="summarize_input" />
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167 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
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168 </test>
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169 <!-- Test grooming from solexa -->
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170 <test>
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171 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
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172 <param name="input_type" value="solexa" />
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173 <param name="options_type_selector" value="advanced" />
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174 <param name="output_type" value="solexa" />
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175 <param name="force_quality_encoding" value="None" />
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176 <param name="summarize_input" value="summarize_input" />
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177 <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" />
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178 </test>
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179 <test>
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180 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
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parents:
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181 <param name="input_type" value="solexa" />
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parents:
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182 <param name="options_type_selector" value="advanced" />
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parents:
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183 <param name="output_type" value="illumina" />
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parents:
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184 <param name="force_quality_encoding" value="None" />
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parents:
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185 <param name="summarize_input" value="summarize_input" />
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parents:
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186 <output name="output_file" file="solexa_full_range_as_illumina.fastqillumina" />
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parents:
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187 </test>
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parents:
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188 <test>
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parents:
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189 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
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parents:
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190 <param name="input_type" value="solexa" />
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parents:
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191 <param name="options_type_selector" value="advanced" />
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parents:
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192 <param name="output_type" value="sanger" />
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parents:
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193 <param name="force_quality_encoding" value="None" />
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parents:
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194 <param name="summarize_input" value="summarize_input" />
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parents:
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195 <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" />
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parents:
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196 </test>
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parents:
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197 <test>
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parents:
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198 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
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parents:
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199 <param name="input_type" value="solexa" />
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parents:
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200 <param name="options_type_selector" value="advanced" />
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parents:
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201 <param name="output_type" value="cssanger" />
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parents:
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202 <param name="force_quality_encoding" value="None" />
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parents:
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203 <param name="summarize_input" value="summarize_input" />
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parents:
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204 <output name="output_file" file="solexa_full_range_as_cssanger.fastqcssanger" />
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parents:
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205 </test>
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parents:
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206 <!-- Test grooming from cssanger -->
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parents:
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207 <test>
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parents:
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208 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
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parents:
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209 <param name="input_type" value="cssanger" />
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parents:
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210 <param name="options_type_selector" value="advanced" />
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parents:
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211 <param name="output_type" value="cssanger" />
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parents:
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212 <param name="force_quality_encoding" value="None" />
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parents:
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213 <param name="summarize_input" value="summarize_input" />
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parents:
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214 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
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parents:
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215 </test>
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parents:
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216 <test>
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parents:
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217 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
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parents:
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218 <param name="input_type" value="cssanger" />
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parents:
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219 <param name="options_type_selector" value="advanced" />
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parents:
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220 <param name="output_type" value="sanger" />
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parents:
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221 <param name="force_quality_encoding" value="None" />
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parents:
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222 <param name="summarize_input" value="summarize_input" />
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parents:
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223 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
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parents:
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224 </test>
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parents:
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225 <test>
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parents:
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226 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
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parents:
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227 <param name="input_type" value="cssanger" />
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parents:
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228 <param name="options_type_selector" value="advanced" />
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parents:
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229 <param name="output_type" value="illumina" />
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parents:
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230 <param name="force_quality_encoding" value="None" />
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parents:
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231 <param name="summarize_input" value="summarize_input" />
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parents:
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232 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
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parents:
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233 </test>
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parents:
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234 <test>
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parents:
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235 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
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parents:
diff changeset
236 <param name="input_type" value="cssanger" />
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parents:
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237 <param name="options_type_selector" value="advanced" />
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parents:
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238 <param name="output_type" value="solexa" />
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parents:
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239 <param name="force_quality_encoding" value="None" />
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parents:
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240 <param name="summarize_input" value="summarize_input" />
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parents:
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241 <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" />
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parents:
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242 </test>
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parents:
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243 <test>
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parents:
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244 <param name="input_file" value="sanger_full_range_as_cssanger_adapter_base_with_quality_score.fastqcssanger_fake_score" ftype="fastq" />
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parents:
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245 <param name="input_type" value="cssanger" />
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parents:
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246 <param name="options_type_selector" value="advanced" />
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parents:
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247 <param name="output_type" value="cssanger" />
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parents:
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248 <param name="force_quality_encoding" value="None" />
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parents:
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249 <param name="summarize_input" value="summarize_input" />
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parents:
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250 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
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parents:
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251 </test>
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parents:
diff changeset
252 <!-- Test fastq with line wrapping -->
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parents:
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253 <test>
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parents:
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254 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
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parents:
diff changeset
255 <param name="input_type" value="sanger" />
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parents:
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256 <param name="options_type_selector" value="advanced" />
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parents:
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257 <param name="output_type" value="sanger" />
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parents:
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258 <param name="force_quality_encoding" value="None" />
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parents:
diff changeset
259 <param name="summarize_input" value="summarize_input" />
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parents:
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260 <output name="output_file" file="wrapping_as_sanger.fastqsanger" />
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parents:
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261 </test>
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parents:
diff changeset
262 <test>
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parents:
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263 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
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parents:
diff changeset
264 <param name="input_type" value="sanger" />
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parents:
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265 <param name="options_type_selector" value="advanced" />
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parents:
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266 <param name="output_type" value="illumina" />
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parents:
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267 <param name="force_quality_encoding" value="None" />
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parents:
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268 <param name="summarize_input" value="summarize_input" />
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parents:
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269 <output name="output_file" file="wrapping_as_illumina.fastqillumina" />
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parents:
diff changeset
270 </test>
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parents:
diff changeset
271 <test>
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parents:
diff changeset
272 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
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parents:
diff changeset
273 <param name="input_type" value="sanger" />
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parents:
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274 <param name="options_type_selector" value="advanced" />
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parents:
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275 <param name="output_type" value="solexa" />
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parents:
diff changeset
276 <param name="force_quality_encoding" value="None" />
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parents:
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277 <param name="summarize_input" value="summarize_input" />
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parents:
diff changeset
278 <output name="output_file" file="wrapping_as_solexa.fastqsolexa" />
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parents:
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279 </test>
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parents:
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280 <!-- Test forcing quality score encoding -->
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parents:
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281 <!-- Sanger, range 0 - 93 -->
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parents:
diff changeset
282 <test>
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parents:
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283 <param name="input_file" value="sanger_full_range_as_decimal_sanger.fastqsanger" ftype="fastq" />
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parents:
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284 <param name="input_type" value="sanger" />
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parents:
diff changeset
285 <param name="options_type_selector" value="advanced" />
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parents:
diff changeset
286 <param name="output_type" value="sanger" />
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parents:
diff changeset
287 <param name="force_quality_encoding" value="ascii" />
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parents:
diff changeset
288 <param name="summarize_input" value="summarize_input" />
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parents:
diff changeset
289 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
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parents:
diff changeset
290 </test>
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parents:
diff changeset
291 <test>
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parents:
diff changeset
292 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
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parents:
diff changeset
293 <param name="input_type" value="sanger" />
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parents:
diff changeset
294 <param name="options_type_selector" value="advanced" />
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parents:
diff changeset
295 <param name="output_type" value="sanger" />
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parents:
diff changeset
296 <param name="force_quality_encoding" value="decimal" />
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parents:
diff changeset
297 <param name="summarize_input" value="summarize_input" />
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parents:
diff changeset
298 <output name="output_file" file="sanger_full_range_as_decimal_sanger.fastqsanger" />
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parents:
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299 </test>
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parents:
diff changeset
300 <test>
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parents:
diff changeset
301 <param name="input_file" value="sanger_full_range_as_tab_decimal_sanger.fastqsanger" ftype="fastq" />
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parents:
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302 <param name="input_type" value="sanger" />
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parents:
diff changeset
303 <param name="options_type_selector" value="advanced" />
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parents:
diff changeset
304 <param name="output_type" value="sanger" />
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parents:
diff changeset
305 <param name="force_quality_encoding" value="ascii" />
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parents:
diff changeset
306 <param name="summarize_input" value="summarize_input" />
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parents:
diff changeset
307 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
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parents:
diff changeset
308 </test>
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parents:
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309 <!-- Solexa, range -5 - 62 -->
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parents:
diff changeset
310 <test>
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parents:
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311 <param name="input_file" value="solexa_full_range_as_decimal_solexa.fastqsolexa" ftype="fastq" />
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parents:
diff changeset
312 <param name="input_type" value="solexa" />
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parents:
diff changeset
313 <param name="options_type_selector" value="advanced" />
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parents:
diff changeset
314 <param name="output_type" value="solexa" />
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parents:
diff changeset
315 <param name="force_quality_encoding" value="ascii" />
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parents:
diff changeset
316 <param name="summarize_input" value="summarize_input" />
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parents:
diff changeset
317 <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" />
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parents:
diff changeset
318 </test>
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parents:
diff changeset
319 <test>
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parents:
diff changeset
320 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
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parents:
diff changeset
321 <param name="input_type" value="solexa" />
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parents:
diff changeset
322 <param name="options_type_selector" value="advanced" />
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parents:
diff changeset
323 <param name="output_type" value="solexa" />
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parents:
diff changeset
324 <param name="force_quality_encoding" value="decimal" />
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parents:
diff changeset
325 <param name="summarize_input" value="summarize_input" />
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parents:
diff changeset
326 <output name="output_file" file="solexa_full_range_as_decimal_solexa.fastqsolexa" />
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parents:
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327 </test>
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parents:
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328 </tests>
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parents:
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329 <help>
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parents:
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330 **What it does**
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parents:
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331
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parents:
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332 This tool offers several conversions options relating to the FASTQ format.
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parents:
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333
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parents:
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334 When using *Basic* options, the output will be *sanger* formatted or *cssanger* formatted (when the input is Color Space Sanger).
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parents:
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335
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parents:
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336 When converting, if a quality score falls outside of the target score range, it will be coerced to the closest available value (i.e. the minimum or maximum).
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parents:
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337
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parents:
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338 When converting between Solexa and the other formats, quality scores are mapped between Solexa and PHRED scales using the equations found in `Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.`_
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parents:
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339
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parents:
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340 When converting between color space (csSanger) and base/sequence space (Sanger, Illumina, Solexa) formats, adapter bases are lost or gained; if gained, the base 'G' is used as the adapter. You cannot convert a color space read to base space if there is no adapter present in the color space sequence. Any masked or ambiguous nucleotides in base space will be converted to 'N's when determining color space encoding.
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parents:
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341
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parents:
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342 -----
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parents:
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343
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parents:
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344 **Quality Score Comparison**
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parents:
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345
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parents:
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346 ::
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parents:
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347
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parents:
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348 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
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parents:
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349 ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
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parents:
diff changeset
350 ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
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parents:
diff changeset
351 !"#$%&amp;'()*+,-./0123456789:;&lt;=&gt;?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
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parents:
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352 | | | | | |
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parents:
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353 33 59 64 73 104 126
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parents:
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354
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parents:
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355 S - Sanger Phred+33, 93 values (0, 93) (0 to 60 expected in raw reads)
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356 I - Illumina 1.3 Phred+64, 62 values (0, 62) (0 to 40 expected in raw reads)
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357 X - Solexa Solexa+64, 67 values (-5, 62) (-5 to 40 expected in raw reads)
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358
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359 Diagram adapted from http://en.wikipedia.org/wiki/FASTQ_format
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360
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361 ------
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362
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363 **Citation**
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364
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365 If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20562416&gt;`_
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366
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367
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368 .. _Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.: http://www.ncbi.nlm.nih.gov/pubmed/20015970
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369
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370 </help>
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371 </tool>