[2] | 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="input3" value="rr.csfasta" ftype="csfasta"/> |
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| 58 | <param name="input4" value="rr.qualsolid" ftype="qualsolid" /> |
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| 59 | <param name="paired" value="yes"/> |
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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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