/tools/emboss_5/emboss_isochore.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 88 lines · 53 code · 19 blank · 16 comment · 0 complexity · 13687829c173d9b2bd8f81875d0753a1 MD5 · raw file

  1. <tool id="EMBOSS: isochore47" name="isochore" version="5.0.0">
  2. <description>Plots isochores in large DNA sequences</description>
  3. <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  4. <command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence $input1 -outfile $ofile2 -goutfile $ofile1 -graph png -window $window -shift $shift -auto</command>
  5. <!-- <command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence $input1 -goutfile $ofile1 -graph png -window $window -shift $shift -auto</command>-->
  6. <inputs>
  7. <param format="fasta" name="input1" type="data">
  8. <label>Sequences</label>
  9. </param>
  10. <param name="window" size="4" type="text" value="1000">
  11. <label>Window size</label>
  12. </param>
  13. <param name="shift" size="4" type="text" value="100">
  14. <label>Shift increment</label>
  15. </param>
  16. </inputs>
  17. <outputs>
  18. <data format="png" name="ofile1" />
  19. <data format="isochore" name="ofile2" />
  20. </outputs>
  21. <!-- <tests>
  22. <test>
  23. <param name="input1" value="2.fasta"/>
  24. <param name="window" value="1000"/>
  25. <param name="shift" value="100"/>
  26. <output name="ofile1" file="emboss_isochore_out.isochore"/>
  27. <output name="ofile2" file="emboss_isochore_out.isochore"/>
  28. </test>
  29. <test>
  30. <param name="input1" value="2.fasta"/>
  31. <param name="window" value="1000"/>
  32. <param name="shift" value="100"/>
  33. <output name="ofile2" file="emboss_isochore_out.isochore"/>
  34. </test>
  35. </tests>-->
  36. <help>
  37. .. class:: warningmark
  38. The input dataset needs to be sequences.
  39. -----
  40. **Syntax**
  41. This application plots GC content over a sequence. It is intended for large sequences such as complete chromosomes or large genomic contigs, although interesting results can also be obtained from shorter sequences. You can view the original documentation here_.
  42. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/isochore.html
  43. - Both **Window size** and **Shift increment** are intergers.
  44. -----
  45. **Example**
  46. - Input sequences::
  47. >hg18_dna range=chrX:151073054-151073376 5'pad=0 3'pad=0 revComp=FALSE strand=? repeatMasking=none
  48. TTTATGTCTATAATCCTTACCAAAAGTTACCTTGGAATAAGAAGAAGTCA
  49. GTAAAAAGAAGGCTGTTGTTCCGTGAAATACTGTCTTTATGCCTCAGATT
  50. TGGAGTGCTCAGAGCCTCTGCAGCAAAGATTTGGCATGTGTCCTAGGCCT
  51. GCTCAGAGCAGCAAATCCCACCCTCTTGGAGAATGAGACTCATAGAGGGA
  52. CAGCTCCCTCCTCAGAGGCTTCTCTAATGGGACTCCAAAGAGCAAACACT
  53. CAGCCCCATGAGGACTGGCCAGGCCAAGTGGTGTGTGGGAACAGGGAGCA
  54. GCGGTTTCCAAGAGGATACAGTA
  55. - Output data file::
  56. Position Percent G+C 1 .. 323
  57. 80 0.422
  58. 112 0.460
  59. 144 0.509
  60. 176 0.534
  61. 208 0.553
  62. 240 0.553
  63. - Output graphics file:
  64. .. image:: ./static/emboss_icons/isochore.png
  65. ------
  66. **Citation**
  67. If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
  68. </help>
  69. </tool>