Mercurial > repos > xuebing > sharplabtool
diff tools/next_gen_conversion/solid_to_fastq.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/next_gen_conversion/solid_to_fastq.xml Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,101 @@ +<tool id="solid_to_fastq" name="SOLiD-to-FASTQ" version="1.0.0"> + <description>converts SOLiD data to FASTQ data</description> + <command interpreter="python"> + solid_to_fastq.py + --input1=$input1 + --input2=$input2 + #if $paired.pairedSingle == "single": + --input3="None" + --input4="None" + #else: + --input3=$input3 + --input4=$input4 + #end if + --output1=$output1 + #if $paired.pairedSingle == "single": + --output2="None" + #else: + --output2=$output2 + #end if + </command> + <inputs> + <conditional name="paired"> + <param name="pairedSingle" type="select" label="Is this library mate-paired?"> + <option value="single">Single</option> + <option value="paired">Paired</option> + </param> + <when value="single"> + <param name="input1" type="data" format="csfasta" label="F3 read file" /> + <param name="input2" type="data" format="qualsolid" label="F3 qual file" /> + </when> + <when value="paired"> + <param name="input1" type="data" format="csfasta" label="F3 read file" /> + <param name="input2" type="data" format="qualsolid" label="F3 qual file" /> + <param name="input3" type="data" format="csfasta" label="R3 read file" /> + <param name="input4" type="data" format="qualsolid" label="R3 qual file" /> + </when> + </conditional> + </inputs> + <outputs> + <!-- Variable number of outputs. Either one (for single-end) or two (for paired-end) --> + <data name="output1" format="fastqsanger"/> + <data name="output2" format="fastqsanger"> + <filter>paired['pairedSingle'] == 'paired'</filter> + </data> + </outputs> + <tests> + <test> + <param name="pairedSingle" value="single" /> + <param name="input1" value="s2fq_phiX.csfasta" ftype="csfasta" /> + <param name="input2" value="s2fq_phiX.qualsolid" ftype="qualsolid" /> + <output name="output1" file="s2fq_out1.fastqsanger" /> + </test> + <test> + <param name="pairedSingle" value="paired" /> + <param name="input1" value="s2fq_paired_F3.csfasta" ftype="csfasta" /> + <param name="input2" value="s2fq_paired_F3_QV.qualsolid" ftype="qualsolid" /> + <param name="input3" value="s2fq_paired_R3.csfasta" ftype="csfasta" /> + <param name="input4" value="s2fq_paired_R3_QV.qualsolid" ftype="qualsolid" /> + <output name="output1" file="s2fq_out2.fastqsanger" /> + <!-- testing framework does not deal with multiple outputs yet + <output name="output2" file="s2fq_out3.fastqsanger" /> + --> + </test> + </tests> + <help> + +**What it does** + +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. + +----- + +**Example** + +- Converting the following sequences:: + + >1831_573_1004_F3 + T00030133312212111300011021310132222 + >1831_573_1567_F3 + T03330322230322112131010221102122113 + +- and quality scores:: + + >1831_573_1004_F3 + 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 + >1831_573_1567_F3 + 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 + +- will produce the following Sanger FASTQ data:: + + @1831_573_1004/1 + AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG + + + >CCAA9952+C>5C.?C79,=42C292:C(9/-7 + @1831_573_1567/1 + TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT + + + ;@@17?@=>7??@A8?==@4A?A4)A+.'A+'1, + + </help> +</tool>