/tools/next_gen_conversion/fastq_conversions.xml

https://bitbucket.org/h_morita_dbcls/galaxy-central · XML · 133 lines · 126 code · 7 blank · 0 comment · 0 complexity · d5fbdc397c5d3cd0e122eeb5d72e6d13 MD5 · raw file

  1. <tool id="fastq_conversions" name="FASTQ Conversions" version="1.0.0">
  2. <description>converts between FASTQ data and other data formats</description>
  3. <command interpreter="python">
  4. fastq_conversions.py
  5. --command=$conversionType.type
  6. --input=$input
  7. #if $conversionType.type == "sol2std":
  8. --outputFastqsanger=$outputFastqsanger
  9. #else:
  10. --outputFastqsanger="None"
  11. #end if
  12. #if $conversionType.type == "std2sol":
  13. --outputFastqsolexa=$outputFastqsolexa
  14. #else:
  15. --outputFastqsolexa="None"
  16. #end if
  17. #if $conversionType.type == "fq2fa":
  18. --outputFasta=$outputFasta
  19. #else:
  20. --outputFasta="None"
  21. #end if
  22. </command>
  23. <inputs>
  24. <conditional name="conversionType">
  25. <param name="type" type="select" label="What type of conversion do you want to do?">
  26. <option value="sol2std">Solexa/Illumina FASTQ to standard Sanger FASTQ</option>
  27. <option value="std2sol">Standard Sanger FASTQ to Solexa/Illumina FASTQ</option>
  28. <option value="fq2fa">Various FASTQ to FASTA</option>
  29. </param>
  30. <when value="sol2std">
  31. <param name="input" type="data" format="fastqsolexa" label="File to convert" />
  32. </when>
  33. <when value="std2sol">
  34. <param name="input" type="data" format="fastqsanger" label="File to convert" />
  35. </when>
  36. <when value="fq2fa">
  37. <param name="input" type="data" format="fastqsolexa, fastqsanger" label="File to convert" />
  38. </when>
  39. </conditional>
  40. </inputs>
  41. <outputs>
  42. <data name="outputFastqsanger" format="fastqsanger">
  43. <filter>conversionType['type'] == 'sol2std'</filter>
  44. </data>
  45. <data name="outputFastqsolexa" format="fastqsolexa">
  46. <filter>conversionType['type'] == 'std2sol'</filter>
  47. </data>
  48. <data name="outputFasta" format="fasta">
  49. <filter>conversionType['type'] == 'fq2fa'</filter>
  50. </data>
  51. </outputs>
  52. <tests>
  53. <test>
  54. <param name="type" value="sol2std" />
  55. <param name="input" value="fastq_conv_in1.fastq" ftype="fastqsolexa" />
  56. <output name="outputFastqsanger" file="fastq_conv_out1.fastqsanger" />
  57. </test>
  58. <test>
  59. <param name="type" value="std2sol" />
  60. <param name="input" value="1.fastqsanger" ftype="fastqsanger" />
  61. <output name="outputFastqsolexa" file="fastq_conv_out2.fastqsolexa" />
  62. </test>
  63. <test>
  64. <param name="type" value="fq2fa" />
  65. <param name="input" value="1.fastqsanger" ftype="fastqsanger" />
  66. <output name="outputFasta" file="fastq_conv_out4.fasta" />
  67. </test>
  68. </tests>
  69. <help>
  70. **What it does**
  71. This tool offers several conversions options relating to the FASTQ format.
  72. -----
  73. **Examples**
  74. - Converting the Solexa/Illumina FASTQ data::
  75. @081017-and-081020:1:1:1715:1759
  76. GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
  77. +
  78. II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&amp;&amp;B
  79. - will produce the following Sanger FASTQ data::
  80. @081017-and-081020:1:1:1715:1759
  81. GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
  82. +
  83. ++!+++++++!!!!!"+++++++!!!!)!%!!+!!%!
  84. - Converting standard Sanger FASTQ::
  85. @1831_573_1004/1
  86. AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
  87. +
  88. >&lt;C&amp;&amp;9952+C>5&lt;.?&lt;79,=42&lt;292:&lt;(9/-7
  89. @1831_573_1050/1
  90. TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
  91. +
  92. ;@@17?@=>7??@A8?==@4A?A4)&amp;+.'&amp;+'1,
  93. - will produce the following Solexa/Illumina FASTQ data::
  94. @1831_573_1004/1
  95. AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
  96. +
  97. ][bEEXXTQJb]T[M^[VXK\SQ[QXQY[GXNLV
  98. @1831_573_1050/1
  99. TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
  100. +
  101. Z__PV^_\]V^^_`W^\\_S`^`SHEJMFEJFPK
  102. - Converting the Sanger FASTQ data::
  103. @1831_573_1004/1
  104. AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
  105. +
  106. >&lt;C&amp;&amp;9952+C>5&lt;.?&lt;79,=42&lt;292:&lt;(9/-7
  107. @1831_573_1050/1
  108. TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
  109. +
  110. ;@@17?@=>7??@A8?==@4A?A4)&amp;+.'&amp;+'1,
  111. - will produce the following FASTA data::
  112. >1831_573_1004/1
  113. AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG
  114. >1831_573_1050/1
  115. TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT
  116. </help>
  117. </tool>