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155 lines
6.0 KiB
XML
155 lines
6.0 KiB
XML
<tool id="solid2fastq" name="Convert" version="1.0.0">
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<description>SOLiD output to fastq</description>
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<command interpreter="python">
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#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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#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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#end if#
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</command>
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<inputs>
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<param name="input1" type="data" format="csfasta" label="Select reads"/>
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<param name="input2" type="data" format="qualsolid" label="Select qualities"/>
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<conditional name="is_run">
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<param name="paired" type="select" label="Is this a mate-pair run?">
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<option value="no" selected="true">No</option>
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<option value="yes">Yes</option>
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</param>
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<when value="yes">
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<param name="input3" type="data" format="csfasta" label="Select Reverse reads"/>
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<param name="input4" type="data" format="qualsolid" label="Select Reverse qualities"/>
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</when>
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<when value="no">
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</when>
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</conditional>
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<param name="qual" label="Remove reads containing color qualities below this value" type="integer" value="0"/>
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<param name="trim_name" type="select" label="Trim trailing "_F3" and "_R3" ?">
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<option value="-t" selected="true">Yes</option>
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<option value="">No</option>
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</param>
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<param name="trim_first_base" type="select" label="Trim first base?">
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<option value="-f">Yes (BWA)</option>
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<option value="" selected="true">No (bowtie)</option>
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</param>
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<param name="double_encode" type="select" label="Double encode?">
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<option value="-d">Yes (BWA)</option>
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<option value="" selected="true">No (bowtie)</option>
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</param>
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</inputs>
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<outputs>
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<data format="fastqcssanger" name="out_file1"/>
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<data format="fastqcssanger" name="out_file2">
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<filter>is_run['paired'] == 'yes'</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="input1" value="fr.csfasta" ftype="csfasta"/>
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<param name="input2" value="fr.qualsolid" ftype="qualsolid" />
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<param name="paired" value="no"/>
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<param name="qual" value="0" />
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<param name="trim_first_base" value="No (bowtie)" />
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<param name="trim_name" value="No" />
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<param name="double_encode" value="No (bowtie)"/>
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<output name="out_file1" file="solid2fastq_out_1.fastq"/>
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</test>
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<test>
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<param name="input1" value="fr.csfasta" ftype="csfasta"/>
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<param name="input2" value="fr.qualsolid" ftype="qualsolid" />
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<param name="paired" value="yes"/>
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<param name="input3" value="rr.csfasta" ftype="csfasta"/>
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<param name="input4" value="rr.qualsolid" ftype="qualsolid" />
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<param name="qual" value="0" />
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<param name="trim_first_base" value="No (bowtie)" />
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<param name="trim_name" value="Yes" />
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<param name="double_encode" value="No (bowtie)"/>
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<output name="out_file1" file="solid2fastq_out_2.fastq"/>
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<output name="out_file2" file="solid2fastq_out_3.fastq"/>
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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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Converts output of SOLiD instrument (versions 3.5 and earlier) to fastq format suitable for bowtie, bwa, and PerM mappers.
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--------
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**Input datasets**
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Below are examples of forward (F3) reads and quality scores:
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Reads::
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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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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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**Mate pairs**
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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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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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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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------
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**Explanation of parameters**
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**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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**Trim trailing "_F3" and "_R3"?** - does just that. Not necessary for bowtie. Required for BWA.
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**Trim first base?** - SOLiD reads contain an adapter base such as the first T in this read::
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>1831_573_1004_F3
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T00030133312212111300011021310132222
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this option removes this base leaving only color calls. Not necessary for bowtie. Required for BWA.
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**Double encode?** - converts color calls (0123.) to pseudo-nucleotides (ACGTN). Not necessary for bowtie. Required for BWA.
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------
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**Examples of output**
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When all parameters are left "as-is" you will get this (using reads and qualities shown above)::
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@1831_573_1004
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T00030133312212111300011021310132222
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+
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%%>CCAA9952+C>5C.?C79,=42C292:C(9/-7
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@1831_573_1004
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T03330322230322112131010221102122113
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+
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);@@17?@=>7??@A8?==@4A?A4)A+.'A+'1,
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Setting *Trim first base from reads* to **Yes** will produce this::
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@1831_573_1004
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00030133312212111300011021310132222
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+
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%%>CCAA9952+C>5C.?C79,=42C292:C(9/-7
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@1831_573_1004
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03330322230322112131010221102122113
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+
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);@@17?@=>7??@A8?==@4A?A4)A+.'A+'1,
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Finally, setting *Double encode* to **Yes** will yield::
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@1831_573_1004
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TAAATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
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+
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%%>CCAA9952+C>5C.?C79,=42C292:C(9/-7
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@1831_573_1004
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TATTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
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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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