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102 lines
3.5 KiB
XML
102 lines
3.5 KiB
XML
<tool id="solid_to_fastq" name="SOLiD-to-FASTQ" version="1.0.0">
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<description>converts SOLiD data to FASTQ data</description>
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<command interpreter="python">
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solid_to_fastq.py
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--input1=$input1
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--input2=$input2
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#if $paired.pairedSingle == "single":
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--input3="None"
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--input4="None"
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#else:
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--input3=$input3
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--input4=$input4
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#end if
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--output1=$output1
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#if $paired.pairedSingle == "single":
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--output2="None"
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#else:
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--output2=$output2
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#end if
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</command>
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<inputs>
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<conditional name="paired">
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<param name="pairedSingle" type="select" label="Is this library mate-paired?">
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<option value="single">Single</option>
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<option value="paired">Paired</option>
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</param>
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<when value="single">
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<param name="input1" type="data" format="csfasta" label="F3 read file" />
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<param name="input2" type="data" format="qualsolid" label="F3 qual file" />
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</when>
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<when value="paired">
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<param name="input1" type="data" format="csfasta" label="F3 read file" />
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<param name="input2" type="data" format="qualsolid" label="F3 qual file" />
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<param name="input3" type="data" format="csfasta" label="R3 read file" />
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<param name="input4" type="data" format="qualsolid" label="R3 qual file" />
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</when>
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</conditional>
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</inputs>
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<outputs>
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<!-- Variable number of outputs. Either one (for single-end) or two (for paired-end) -->
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<data name="output1" format="fastqsanger"/>
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<data name="output2" format="fastqsanger">
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<filter>paired['pairedSingle'] == 'paired'</filter>
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</data>
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</outputs>
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<tests>
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<test>
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<param name="pairedSingle" value="single" />
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<param name="input1" value="s2fq_phiX.csfasta" ftype="csfasta" />
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<param name="input2" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
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<output name="output1" file="s2fq_out1.fastqsanger" />
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</test>
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<test>
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<param name="pairedSingle" value="paired" />
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<param name="input1" value="s2fq_paired_F3.csfasta" ftype="csfasta" />
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<param name="input2" value="s2fq_paired_F3_QV.qualsolid" ftype="qualsolid" />
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<param name="input3" value="s2fq_paired_R3.csfasta" ftype="csfasta" />
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<param name="input4" value="s2fq_paired_R3_QV.qualsolid" ftype="qualsolid" />
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<output name="output1" file="s2fq_out2.fastqsanger" />
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<!-- testing framework does not deal with multiple outputs yet
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<output name="output2" file="s2fq_out3.fastqsanger" />
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-->
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</test>
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</tests>
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<help>
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**What it does**
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This tool takes reads and quality files and converts them to FASTQ data ( Sanger variant ). Any -1 qualities are converted to 1 before being converted to FASTQ. Note that it also converts sequences to base pairs.
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-----
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**Example**
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- Converting the following sequences::
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>1831_573_1004_F3
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T00030133312212111300011021310132222
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>1831_573_1567_F3
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T03330322230322112131010221102122113
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- and quality scores::
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>1831_573_1004_F3
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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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>1831_573_1567_F3
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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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- will produce the following Sanger FASTQ data::
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@1831_573_1004/1
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AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
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+
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>CCAA9952+C>5C.?C79,=42C292:C(9/-7
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@1831_573_1567/1
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TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
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+
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;@@17?@=>7??@A8?==@4A?A4)A+.'A+'1,
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</help>
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</tool>
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