/tools/fastq/fastq_paired_end_splitter.xml
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1<tool id="fastq_paired_end_splitter" name="FASTQ splitter" version="1.0.0"> 2 <description>on joined paired end reads</description> 3 <command interpreter="python">fastq_paired_end_splitter.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$output1_file' '$output2_file'</command> 4 <inputs> 5 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ reads" /> 6 </inputs> 7 <outputs> 8 <data name="output1_file" format="input" /> 9 <data name="output2_file" format="input" /> 10 </outputs> 11 <tests> 12 <test> 13 <param name="input1_file" value="3.fastqsanger" ftype="fastqsanger" /> 14 <output name="output1_file" file="split_pair_reads_1.fastqsanger" /> 15 <output name="output2_file" file="split_pair_reads_2.fastqsanger" /> 16 </test> 17 </tests> 18 <help> 19**What it does** 20 21Splits 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. 22 23Sequence identifiers will have /1 or /2 appended for the split left-hand and right-hand reads, respectively. 24 25----- 26 27**Input format** 28 29A multiple-fastq file, for example:: 30 31 @HWI-EAS91_1_30788AAXX:7:21:1542:1758 32 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA 33 +HWI-EAS91_1_30788AAXX:7:21:1542:1758 34 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR 35 36 37----- 38 39**Outputs** 40 41Left-hand Read:: 42 43 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 44 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC 45 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 46 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh 47 48Right-hand Read:: 49 50 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 51 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA 52 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 53 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR 54 55 </help> 56</tool>