/tools/maf/maf_to_interval.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 133 lines · 96 code · 37 blank · 0 comment · 0 complexity · 3e100aab7a468f887087e01d84c40527 MD5 · raw file 

    

  1. <tool id="MAF_To_Interval1" name="MAF to Interval" force_history_refresh="True">
    2. 

  2.   <description>Converts a MAF formatted file to the Interval format</description>
    3. 

  3.   <command interpreter="python">maf_to_interval.py $input1 $out_file1 $out_file1.id $__new_file_path__ $input1.dbkey $species $input1.metadata.species $complete_blocks $remove_gaps</command>
    4. 

  4.   <inputs>
    5. 

  5.     <param format="maf" name="input1" type="data" label="MAF file to convert"/>
    6. 

  6.     <param name="species" type="select" label="Select additional species" display="checkboxes" multiple="true" help="The species matching the dbkey of the alignment is always included. A separate history item will be created for each species.">
    7. 

  7.       <options>
    8. 

  8.         <filter type="data_meta" ref="input1" key="species" />
    9. 

  9.         <filter type="remove_value" meta_ref="input1" key="dbkey" />
    10. 

  10.       </options>
    11. 

  11.     </param>
    12. 

  12.     <param name="complete_blocks" type="select" label="Exclude blocks which have a species missing">
    13. 

  13.       <option value="partial_allowed">include blocks with missing species</option>
    14. 

  14.       <option value="partial_disallowed">exclude blocks with missing species</option>
    15. 

  15.     </param>
    16. 

  16.     <param name="remove_gaps" type="select" label="Remove Gap characters from sequences">
    17. 

  17.       <option value="keep_gaps">keep gaps</option>
    18. 

  18.       <option value="remove_gaps">remove gaps</option>
    19. 

  19.     </param>
    20. 

  20.   </inputs>
    21. 

  21.   <outputs>
    22. 

  22.     <data format="interval" name="out_file1" />
    23. 

  23.   </outputs>
    24. 

  24.   <tests>
    25. 

  25.     <test>
    26. 

  26.       <param name="input1" value="4.maf" dbkey="hg17"/>
    27. 

  27.       <param name="complete_blocks" value="partial_disallowed"/>
    28. 

  28.       <param name="remove_gaps" value="keep_gaps"/>
    29. 

  29.       <param name="species" value="panTro1" />
    30. 

  30.       <output name="out_file1" file="maf_to_interval_out_hg17.interval"/>
    31. 

  31.       <output name="out_file1" file="maf_to_interval_out_panTro1.interval"/>
    32. 

  32.     </test>
    33. 

  33.   </tests>
    34. 

  34.   <help>
    35. 

  35. 

  36. **What it does**
    37. 

  37. 

  38. This tool converts every MAF block to a set of genomic intervals describing the position of that alignment block within a corresponding genome. Sequences from aligning species are also included in the output.
    39. 

  39. 

  40. The interface for this tool contains several options: 
    41. 

  41. 

  42.  * **MAF file to convert**. Choose multiple alignments from history to be converted to BED format.
    43. 

  43.  * **Choose species**. Choose additional species from the alignment to be included in the output 
    44. 

  44.  * **Exclude blocks which have a species missing**. if an alignment block does not contain any one of the species found in the alignment set and this option is set to **exclude blocks with missing species**, then coordinates of such a block **will not** be included in the output (see **Example 2** below).
    45. 

  45.  * **Remove Gap characters from sequences**. Gaps can be removed from sequences before they are output.
    46. 

  46. 

  47. 

  48. -----
    49. 

  49. 

  50. **Example 1**: **Include only reference genome** (hg18 in this case) and **include blocks with missing species**:
    51. 

  51. 

  52. For the following alignment::
    53. 

  53. 

  54.   ##maf version=1
    55. 

  55.   a score=68686.000000
    56. 

  56.   s hg18.chr20     56827368 75 +  62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 
    57. 

  57.   s panTro2.chr20  56528685 75 +  62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 
    58. 

  58.   s rheMac2.chr10  89144112 69 -  94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA------- 
    59. 

  59.   s mm8.chr2      173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- 
    60. 

  60.   s canFam2.chr24  46551822 67 +  50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C 
    61. 

  61. 

  62.   a score=10289.000000
    63. 

  63.   s hg18.chr20    56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 
    64. 

  64.   s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 
    65. 

  65.   s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG 
    66. 

  66. 

  67. the tool will create **a single** history item containing the following (**note** the name field is numbered iteratively: hg18_0_0, hg18_1_0 etc. where the first number is the block number and the second number is the iteration through the block (if a species appears twice in a block, that interval will be repeated) and sequences for each species are included in the order specified in the header: the field is left empty when no sequence is available for that species)::
    68. 

  68. 

  69.   #chrom	start	end	strand	score	name	canFam2	hg18	mm8	panTro2	rheMac2
    70. 

  70.   chr20	56827368	56827443	+	68686.0	hg18_0_0	CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C	GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-	AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------	GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-	GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
    71. 

  71.   chr20	56827443	56827480	+	10289.0	hg18_1_0		ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG		ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG	ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
    72. 

  72. 

  73. 

  74. -----
    75. 

  75. 

  76. **Example 2**: **Include hg18 and mm8** and **exclude blocks with missing species**:
    77. 

  77. 

  78. For the following alignment::
    79. 

  79. 

  80.   ##maf version=1
    81. 

  81.   a score=68686.000000
    82. 

  82.   s hg18.chr20     56827368 75 +  62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 
    83. 

  83.   s panTro2.chr20  56528685 75 +  62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 
    84. 

  84.   s rheMac2.chr10  89144112 69 -  94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA------- 
    85. 

  85.   s mm8.chr2      173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- 
    86. 

  86.   s canFam2.chr24  46551822 67 +  50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C 
    87. 

  87. 

  88.   a score=10289.000000
    89. 

  89.   s hg18.chr20    56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 
    90. 

  90.   s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 
    91. 

  91.   s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG 
    92. 

  92. 

  93. the tool will create **two** history items (one for hg18 and one for mm8) containing the following (**note** that both history items contain only one line describing the first alignment block. The second MAF block is not included in the output because it does not contain mm8):
    94. 

  94. 

  95. History item **1** (for hg18)::
    96. 

  96. 

  97.    #chrom	start	end	strand	score	name	canFam2	hg18	mm8	panTro2	rheMac2
    98. 

  98.    chr20	56827368	56827443	+	68686.0	hg18_0_0	CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C	GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-	AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------	GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-	GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
    99. 

  99. 

  100. 

  101. History item **2** (for mm8)::
    102. 

  102. 

  103.    #chrom	start	end	strand	score	name	canFam2	hg18	mm8	panTro2	rheMac2
    104. 

  104.    chr2	173910832	173910893	+	68686.0	mm8_0_0	CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C	GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-	AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------	GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-	GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
    105. 

  105. 

  106. 

  107. -------
    108. 

  108. 

  109. .. class:: infomark
    110. 

  110. 

  111. **About formats**
    112. 

  112. 

  113. **MAF format** multiple alignment format file. This format stores multiple alignments at the DNA level between entire genomes. 
    114. 

  114. 

  115.  - The .maf format is line-oriented. Each multiple alignment ends with a blank line.
    116. 

  116.  - Each sequence in an alignment is on a single line.
    117. 

  117.  - Lines starting with # are considered to be comments.
    118. 

  118.  - Each multiple alignment is in a separate paragraph that begins with an "a" line and contains an "s" line for each sequence in the multiple alignment.
    119. 

  119.  - Some MAF files may contain two optional line types: 
    120. 

  120. 

  121.    - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line; 
    122. 

  122.    - An "e" line containing information about the size of the gap between the alignments that span the current block.
    123. 

  123. 

  124. ------
    125. 

  125. 

  126. **Citation**
    127. 

  127. 

  128. If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21775304&gt;`_
    129. 

  129. 

  130. 

  131.     </help>
    132. 

  132. </tool>
    133.