/tools/fastq/fastq_paired_end_splitter.xml

https://bitbucket.org/h_morita_dbcls/galaxy-central · XML · 56 lines · 42 code · 14 blank · 0 comment · 0 complexity · c2863d819b63acd2a8c3beac162bcf97 MD5 · raw file

  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. 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.
  21. Sequence identifiers will have /1 or /2 appended for the split left-hand and right-hand reads, respectively.
  22. -----
  23. **Input format**
  24. A multiple-fastq file, for example::
  25. @HWI-EAS91_1_30788AAXX:7:21:1542:1758
  26. GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
  27. +HWI-EAS91_1_30788AAXX:7:21:1542:1758
  28. hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
  29. -----
  30. **Outputs**
  31. Left-hand Read::
  32. @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
  33. GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
  34. +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
  35. hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
  36. Right-hand Read::
  37. @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
  38. GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
  39. +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
  40. hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
  41. </help>
  42. </tool>