/tools/filters/sff_extractor.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 58 lines · 53 code · 5 blank · 0 comment · 0 complexity · 688a504efe92059b62cc226848fbf9eb MD5 · raw file

  1. <tool id="Sff_extractor" name="SFF converter" version="1.0.1">
  2. <description></description>
  3. <command interpreter="python">
  4. #if str($fastq_output) == "fastq_false" #sff_extract.py $clip --seq_file=$out_file3 --qual_file=$out_file4 --xml_file=$out_file2 $input
  5. #elif str($fastq_output) == "fastq_true" #sff_extract.py $clip --fastq --seq_file=$out_file1 --xml_file=$out_file2 $input
  6. #end if#
  7. </command>
  8. <inputs>
  9. <param format="sff" name="input" type="data" label="Extract from this dataset"/>
  10. <param name="clip" type="select" label="Completely remove ends with low qual and/or adaptor sequence">
  11. <option value="">No</option>
  12. <option value="--clip">Yes</option>
  13. </param>
  14. <param name="fastq_output" type="boolean" truevalue="fastq_true" falsevalue="fastq_false" checked="False" label="Do you want FASTQ file instead of FASTA + FASTA quality file?" />
  15. </inputs>
  16. <outputs>
  17. <data format="fastqsanger" name="out_file1" >
  18. <filter>fastq_output is True</filter>
  19. </data>
  20. <data format="xml" name="out_file2">
  21. </data>
  22. <data format="fasta" name="out_file3">
  23. <filter>fastq_output is False</filter>
  24. </data>
  25. <data format="qual" name="out_file4">
  26. <filter>fastq_output is False</filter>
  27. </data>
  28. </outputs>
  29. <tests>
  30. <test>
  31. <param name="input" value="2.sff"/>
  32. <param name="clip" value=""/>
  33. <param name="fastq_output" value="false"/>
  34. <output name="out_file2" file="sff_converter_xml_1.dat"/>
  35. <output name="out_file3" file="sff_converter_fasta.dat"/>
  36. <output name="out_file4" file="sff_converter_qual.dat"/>
  37. </test>
  38. <test>
  39. <param name="input" value="2.sff"/>
  40. <param name="clip" value=""/>
  41. <param name="fastq_output" value="true"/>
  42. <output name="out_file1" file="sff_converter_fastq.dat"/>
  43. <output name="out_file2" file="sff_converter_xml_2.dat"/>
  44. </test>
  45. </tests>
  46. <help>
  47. **What it does**
  48. This tool extracts data from the 454 Sequencer SFF format and creates three files containing the:
  49. Sequences (FASTA),
  50. Qualities (QUAL) and
  51. Clippings (XML)
  52. </help>
  53. </tool>