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/tools/metag_tools/rmapq_wrapper.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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  1. <tool id="rmapq_wrapper" name="RMAPQ" version="1.0.0">
  2. <description>for Solexa Short Reads Alignment with Quality Scores</description>
  3. <command interpreter="python">
  4. #if $trim.choice=="No": #rmapq_wrapper.py $database $input_seq $input_score $high_score $high_len 0 $align_len $mismatch $output1
  5. #else: #rmapq_wrapper.py $database $input_seq $input_score $high_score $high_len $trim.read_len $align_len $mismatch $output1
  6. #end if
  7. </command>
  8. <inputs>
  9. <param name="database" type="select" display="radio" label="Target database">
  10. <options from_file="faseq.loc">
  11. <column name="name" index="0"/>
  12. <column name="value" index="0"/>
  13. </options>
  14. </param>
  15. <param name="input_seq" type="data" format="fasta" label="Sequence file"/>
  16. <param name="input_score" type="data" format="qualsolexa" label="Quality score file"/>
  17. <param name="high_score" type="float" size="15" value="40" label="Minimum score for high-quality base (-q)"/>
  18. <param name="high_len" type="integer" size="15" value="36" label="Minimal high-quality bases (-M)"/>
  19. <param name="align_len" type="integer" size="15" value="11" label="Minimal length of a hit (-h)" help="seed"/>
  20. <param name="mismatch" type="select" label="Number of mismatches allowed (-m)">
  21. <option value="0">0</option>
  22. <option value="1">1</option>
  23. <option value="3">3</option>
  24. <option value="5">5</option>
  25. </param>
  26. <conditional name="trim">
  27. <param name="choice" type="select" label="To trim the reads">
  28. <option value="No">No</option>
  29. <option value="Yes">Yes</option>
  30. </param>
  31. <when value="No">
  32. </when>
  33. <when value="Yes">
  34. <param name="read_len" type="integer" size="15" value="36" label="Read length (-w)" />
  35. </when>
  36. </conditional>
  37. </inputs>
  38. <outputs>
  39. <data name="output1" format="bed"/>
  40. </outputs>
  41. <requirements>
  42. <requirement type="binary">rmapq</requirement>
  43. </requirements>
  44. <!--
  45. <tests>
  46. <test>
  47. <param name="database" value="/galaxy/data/faseq/test" />
  48. <param name="input_seq" value="rmapq_wrapper_test1.fasta" ftype="fasta"/>
  49. <param name="input_score" value="rmapq_wrapper_test1.qual" ftype="qualsolexa" />
  50. <param name="high_score" value="40" />
  51. <param name="high_len" value="36" />
  52. <param name="read_len" value="36" />
  53. <param name="align_len" value="36" />
  54. <param name="mismatch" value="3" />
  55. <output name="output1" file="rmapq_wrapper_test1.bed"/>
  56. </test>
  57. </tests>
  58. -->
  59. <help>
  60. .. class:: warningmark
  61. RMAPQ was developed for **Solexa** reads.
  62. .. class:: infomark
  63. **TIP**. The tool will guess the length of the reads, however, if you select to trim the reads, the *Maximal Length of the Reads* must be between 20 and 64. Reads with lengths longer than the specified value will be trimmed at the 3'end.
  64. -----
  65. **What it does**
  66. This tool runs **rmapq** (for more information, please see the reference below), searching against a genome build with sequence qualities.
  67. -----
  68. **Parameters**
  69. - *Minimal High-quality Bases* (**-M**): the minimal length of the high quality score bases
  70. - *Minimum Score for High-quality Base* (**-q**) : the minimal quality score
  71. - *Minimal Length of a Hit* (**-h**) : the minimal length of an exact match or seed
  72. - *Number of Mismatches Allowed* (**-m**) : the maximal number of mismatches allowed in an alignment
  73. - *Read Length* (**-w**) : maximal length of the reads; reads longer than the threshold will be truncated at 3' end.
  74. -----
  75. **Reference**
  76. **RMAP** is developed by Dr. Andrew D Smith and Dr. Zhenyu Xuan at the Cold Spring Harbor Laboratory. Please see http://rulai.cshl.edu/rmap/
  77. </help>
  78. </tool>