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