/tools/fastx_toolkit/fasta_formatter.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 87 lines · 57 code · 19 blank · 11 comment · 0 complexity · 8b921702d94023ab58dc11d8f4df842c MD5 · raw file

  1. <tool id="cshl_fasta_formatter" name="FASTA Width">
  2. <description>formatter</description>
  3. <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
  4. <!--
  5. Note:
  6. fasta_formatter also has a tabular output mode (-t),
  7. but Galaxy already contains such a tool, so no need
  8. to offer the user a duplicated tool.
  9. So this XML tool only changes the width (line-wrapping) of a
  10. FASTA file.
  11. -->
  12. <command>zcat -f '$input' | fasta_formatter -w $width -o $output</command>
  13. <inputs>
  14. <param format="fasta" name="input" type="data" label="Library to re-format" />
  15. <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." />
  16. </inputs>
  17. <tests>
  18. <test>
  19. <!-- Re-format a FASTA file into a single line -->
  20. <param name="input" value="fasta_formatter1.fasta" />
  21. <param name="width" value="0" />
  22. <output name="output" file="fasta_formatter1.out" />
  23. </test>
  24. <test>
  25. <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes -->
  26. <param name="input" value="fasta_formatter1.fasta" />
  27. <param name="width" value="60" />
  28. <output name="output" file="fasta_formatter2.out" />
  29. </test>
  30. </tests>
  31. <outputs>
  32. <data format="input" name="output" metadata_source="input" />
  33. </outputs>
  34. <help>
  35. **What it does**
  36. This tool re-formats a FASTA file, changing the width of the nucleotides lines.
  37. **TIP:** Outputting a single line (with **width = 0**) can be useful for scripting (with **grep**, **awk**, and **perl**). Every odd line is a sequence identifier, and every even line is a nucleotides line.
  38. --------
  39. **Example**
  40. Input FASTA file (each nucleotides line is 50 characters long)::
  41. >Scaffold3648
  42. AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC
  43. CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG
  44. TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA
  45. ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
  46. >Scaffold9299
  47. CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
  48. TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
  49. aactggtctttacctTTAAGTTG
  50. Output FASTA file (with width=80)::
  51. >Scaffold3648
  52. AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTT
  53. ATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCA
  54. ATTTTAATGAACATGTAGTAAAAACT
  55. >Scaffold9299
  56. CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTAC
  57. GTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
  58. Output FASTA file (with width=0 => single line)::
  59. >Scaffold3648
  60. AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
  61. >Scaffold9299
  62. CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
  63. ------
  64. This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
  65. .. __: http://hannonlab.cshl.edu/fastx_toolkit/
  66. </help>
  67. </tool>