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1 <tool id="solid2fastq" name="Convert">
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2 <description>SOLiD output to fastq</description>
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3 <command interpreter="python">
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4 #if $is_run.paired == "no" #solid2fastq.py --fr=$input1 --fq=$input2 --fout=$out_file1 -q $qual $trim_name $trim_first_base $double_encode
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5 #elif $is_run.paired == "yes" #solid2fastq.py --fr=$input1 --fq=$input2 --fout=$out_file1 --rr=$input3 --rq=$input4 --rout=$out_file2 -q $qual $trim_name $trim_first_base $double_encode
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6 #end if#
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7 </command>
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8 <inputs>
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9 <param name="input1" type="data" format="csfasta" label="Select reads"/>
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10 <param name="input2" type="data" format="qualsolid" label="Select qualities"/>
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11 <conditional name="is_run">
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12 <param name="paired" type="select" label="Is this a mate-pair run?">
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13 <option value="no" selected="true">No</option>
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14 <option value="yes">Yes</option>
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15 </param>
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16 <when value="yes">
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17 <param name="input3" type="data" format="csfasta" label="Select Reverse reads"/>
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18 <param name="input4" type="data" format="qualsolid" label="Select Reverse qualities"/>
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19 </when>
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20 <when value="no">
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21 </when>
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22 </conditional>
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23 <param name="qual" label="Remove reads containing color qualities below this value" type="integer" value="0"/>
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24 <param name="trim_name" type="select" label="Trim trailing "_F3" and "_R3" ?">
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25 <option value="-t" selected="true">Yes</option>
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26 <option value="">No</option>
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27 </param>
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28 <param name="trim_first_base" type="select" label="Trim first base?">
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29 <option value="-f">Yes (BWA)</option>
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30 <option value="" selected="true">No (bowtie)</option>
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31 </param>
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32 <param name="double_encode" type="select" label="Double encode?">
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33 <option value="-d">Yes (BWA)</option>
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34 <option value="" selected="true">No (bowtie)</option>
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35 </param>
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36 </inputs>
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37 <outputs>
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38 <data format="fastqcssanger" name="out_file1"/>
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39 <data format="fastqcssanger" name="out_file2">
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40 <filter>is_run['paired'] == 'yes'</filter>
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41 </data>
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="input1" value="fr.csfasta" ftype="csfasta"/>
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46 <param name="input2" value="fr.qualsolid" ftype="qualsolid" />
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47 <param name="paired" value="no"/>
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48 <param name="qual" value="0" />
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49 <param name="trim_first_base" value="No" />
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50 <param name="trim_name" value="No" />
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51 <param name="double_encode" value="No"/>
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52 <output name="out_file1" file="solid2fastq_out_1.fastq"/>
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53 </test>
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54 <test>
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55 <param name="input1" value="fr.csfasta" ftype="csfasta"/>
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56 <param name="input2" value="fr.qualsolid" ftype="qualsolid" />
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57 <param name="paired" value="yes"/>
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58 <param name="input3" value="rr.csfasta" ftype="csfasta"/>
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59 <param name="input4" value="rr.qualsolid" ftype="qualsolid" />
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60 <param name="qual" value="0" />
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61 <param name="trim_first_base" value="No" />
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62 <param name="trim_name" value="Yes" />
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63 <param name="double_encode" value="No"/>
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64 <output name="out_file1" file="solid2fastq_out_2.fastq"/>
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65 <output name="out_file2" file="solid2fastq_out_3.fastq"/>
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66 </test>
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67 </tests>
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68 <help>
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69
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70 **What it does**
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71
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72 Converts output of SOLiD instrument (versions 3.5 and earlier) to fastq format suitable for bowtie, bwa, and PerM mappers.
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73
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74 --------
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75
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76 **Input datasets**
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77
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78 Below are examples of forward (F3) reads and quality scores:
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79
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80 Reads::
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81
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82 >1831_573_1004_F3
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83 T00030133312212111300011021310132222
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84 >1831_573_1567_F3
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85 T03330322230322112131010221102122113
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86
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87 Quality scores::
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88
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89 >1831_573_1004_F3
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90 4 29 34 34 32 32 24 24 20 17 10 34 29 20 34 13 30 34 22 24 11 28 19 17 34 17 24 17 25 34 7 24 14 12 22
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91 >1831_573_1567_F3
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92 8 26 31 31 16 22 30 31 28 29 22 30 30 31 32 23 30 28 28 31 19 32 30 32 19 8 32 10 13 6 32 10 6 16 11
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93
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94
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95 **Mate pairs**
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96
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97 If your data is from a mate-paired run, you will have additional read and quality datasets that will look similar to the ones above with one exception: the names of reads will be ending with "_R3".
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98 In this case choose **Yes** from the *Is this a mate-pair run?* drop down and you will be able to select R reads. When processing mate pairs this tool generates two output files: one for F3 reads and the other for R3 reads.
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99 The reads are guaranteed to be paired -- mated reads will be in the same position in F3 and R3 fastq file. However, because pairing is verified it may take a while to process an entire SOLiD run (several hours).
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100
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101 ------
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102
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103 **Explanation of parameters**
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104
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105 **Remove reads containing color qualities below this value** - any read that contains as least one color call with quality lower than the specified value **will not** be reported.
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106
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107 **Trim trailing "_F3" and "_R3"?** - does just that. Not necessary for bowtie. Required for BWA.
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108
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109 **Trim first base?** - SOLiD reads contain an adapter base such as the first T in this read::
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110
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111 >1831_573_1004_F3
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112 T00030133312212111300011021310132222
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113
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114 this option removes this base leaving only color calls. Not necessary for bowtie. Required for BWA.
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115
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116 **Double encode?** - converts color calls (0123.) to pseudo-nucleotides (ACGTN). Not necessary for bowtie. Required for BWA.
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117
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118 ------
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119
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120 **Examples of output**
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121
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122 When all parameters are left "as-is" you will get this (using reads and qualities shown above)::
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123
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124 @1831_573_1004
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125 T00030133312212111300011021310132222
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126 +
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127 %>CCAA9952+C>5C.?C79,=42C292:C(9/-7
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128 @1831_573_1004
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129 T03330322230322112131010221102122113
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130 +
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131 );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1,
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132
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133 Setting *Trim first base from reads* to **Yes** will produce this::
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134
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135 @1831_573_1004
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136 00030133312212111300011021310132222
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137 +
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138 %>CCAA9952+C>5C.?C79,=42C292:C(9/-7
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139 @1831_573_1004
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140 03330322230322112131010221102122113
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141 +
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142 );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1,
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143
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144 Finally, setting *Double encode* to **Yes** will yield::
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145
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146 @1831_573_1004
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147 TAAATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
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148 +
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149 %>CCAA9952+C>5C.?C79,=42C292:C(9/-7
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150 @1831_573_1004
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151 TATTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
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152 +
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153 );@@17?@=>7??@A8?==@4A?A4)A+.'A+'1,
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154
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155
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156
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157
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158
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159 </help>
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160 </tool>
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