Mercurial > repos > devteam > split_paired_reads
diff split_paired_reads.xml @ 0:e7d1ffdbb9b6 draft default tip
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author | devteam |
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date | Wed, 21 Aug 2013 13:20:57 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/split_paired_reads.xml Wed Aug 21 13:20:57 2013 -0400 @@ -0,0 +1,57 @@ +<tool id="split_paired_reads" name="Split paired end reads" version="1.0.0"> + <description></description> + <command interpreter="python"> + split_paired_reads.py $input $output1 $output2 + </command> + <inputs> + <param name="input" type="data" format="fastqsanger" label="Your paired-end file" /> + </inputs> + <outputs> + <data name="output1" format="fastqsanger"/> + <data name="output2" format="fastqsanger"/> + </outputs> + <tests> + <test> + <param name="input" value="3.fastqsanger" ftype="fastqsanger"/> + <output name="output1" file="split_pair_reads_1.fastqsanger" ftype="fastqsanger"/> + <output name="output2" file="split_pair_reads_2.fastqsanger" ftype="fastqsanger"/> + </test> + </tests> +<help> + +**What it does** + +Splits a single fastq dataset representing paired-end run into two datasets (one for each end). This tool works only for datasets where both ends have **the same** length. + +----- + +**Input formats** + +A multiple-fastq file, for example:: + + @HWI-EAS91_1_30788AAXX:7:21:1542:1758 + GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA + +HWI-EAS91_1_30788AAXX:7:21:1542:1758 + hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR + + +----- + +**Outputs** + +One end:: + + @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 + GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC + +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 + hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh + +The other end:: + + @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 + GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA + +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 + hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR + +</help> +</tool>