root/galaxy-central/tools/maf/maf_to_fasta.xml @ 3

<tool id="MAF_To_Fasta1" name="MAF to FASTA" version="1.0.1">
  <description>Converts a MAF formated file to FASTA format</description>
  <command interpreter="python">
    #if $fasta_target_type.fasta_type == "multiple" #maf_to_fasta_multiple_sets.py $input1 $out_file1 $fasta_target_type.species $fasta_target_type.complete_blocks
    #else                                           #maf_to_fasta_concat.py $fasta_target_type.species $input1 $out_file1
    #end if#
  </command>
  <inputs>
    <param format="maf" name="input1" type="data" label="MAF file to convert"/>
    <conditional name="fasta_target_type">
      <param name="fasta_type" type="select" label="Type of FASTA Output">
        <option value="multiple" selected="true">Multiple Blocks</option>
        <option value="concatenated">One Sequence per Species</option>
      </param>
      <when value="multiple">
        <param name="species" type="select" label="Select species" display="checkboxes" multiple="true" help="checked taxa will be included in the output">
          <options>
            <filter type="data_meta" ref="input1" key="species" />
          </options>
        </param>
            <param name="complete_blocks" type="select" label="Choose to">
              <option value="partial_allowed">include blocks with missing species</option>
              <option value="partial_disallowed">exclude blocks with missing species</option>
            </param>
      </when>
      <when value="concatenated">
        <param name="species" type="select" label="Species to extract" display="checkboxes" multiple="true">
          <options>
            <filter type="data_meta" ref="input1" key="species" />
          </options>
        </param>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="fasta" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="3.maf" ftype="maf"/>
      <param name="species" value="canFam1"/>
      <param name="fasta_type" value="concatenated"/>
      <output name="out_file1" file="cf_maf2fasta_concat.dat" ftype="fasta"/>
    </test>
    <test>
      <param name="input1" value="4.maf" ftype="maf"/>
      <param name="species" value="hg17,panTro1,rheMac2,rn3,mm7,canFam2,bosTau2,dasNov1"/>
      <param name="complete_blocks" value="partial_allowed"/>
      <param name="fasta_type" value="multiple"/>
      <output name="out_file1" file="cf_maf2fasta_new.dat" ftype="fasta"/>
    </test>
  </tests>
  <help>

**Types of MAF to FASTA conversion**

 * **Multiple Blocks** converts a single MAF block to a single FASTA block. For example, if you have 6 MAF blocks, they will be converted to 6 FASTA blocks.
 * **One Sequence per Species** converts MAF blocks to a single aggregated FASTA block. For example, if you have 6 MAF blocks, they will be converted and concatenated into a single FASTA block.

-------

**What it does**

This tool converts MAF blocks to FASTA format and concatenates them into a single FASTA block or outputs multiple FASTA blocks separated by empty lines.

The interface for this tool contains two pages (steps): 

 * **Step 1 of 2**. Choose multiple alignments from history to be converted to FASTA format.
 * **Step 2 of 2**. Choose the type of output as well as the species from the alignment to be included in the output.
 
   Multiple Block output has additional options:
   
   *  **Choose species** - the tool reads the alignment provided during Step 1 and generates a list of species contained within that alignment. Using checkboxes you can specify taxa to be included in the output (all species are selected by default). 
   *  **Choose to include/exclude blocks with missing species** - if an alignment block does not contain any one of the species you selected within **Choose species** menu and this option is set to **exclude blocks with missing species**, then such a block **will not** be included in the output (see **Example 2** below).  For example, if you want to extract human, mouse, and rat from a series of alignments and one of the blocks does not contain mouse sequence, then this block will not be converted to FASTA and will not be returned.


-----

**Example 1**:

In the concatenated approach, the following alignment::

  ##maf version=1
  a score=68686.000000
  s hg18.chr20     56827368 75 +  62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 
  s panTro2.chr20  56528685 75 +  62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 
  s rheMac2.chr10  89144112 69 -  94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA------- 
  s mm8.chr2      173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- 
  s canFam2.chr24  46551822 67 +  50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C 

  a score=10289.000000
  s hg18.chr20    56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 
  s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 
  s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG 

will be converted to (**note** that because mm8 (mouse) and canFam2 (dog) are absent from the second block, they are replaced with gaps after concatenation)::

  &gt;canFam2
  CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C-------------------------------------
  &gt;hg18
  GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
  &gt;mm8
  AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC--------------------------------------------
  &gt;panTro2
  GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
  &gt;rheMac2
  GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG

------

**Example 2a**: Multiple Block Approach **Include all species** and **include blocks with missing species**:

The following alignment::

  ##maf version=1
  a score=68686.000000
  s hg18.chr20     56827368 75 +  62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 
  s panTro2.chr20  56528685 75 +  62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 
  s rheMac2.chr10  89144112 69 -  94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA------- 
  s mm8.chr2      173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- 
  s canFam2.chr24  46551822 67 +  50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C 

  a score=10289.000000
  s hg18.chr20    56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 
  s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 
  s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG 

will be converted to::

  &gt;hg18.chr20(+):56827368-56827443|hg18_0
  GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
  &gt;panTro2.chr20(+):56528685-56528760|panTro2_0
  GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
  &gt;rheMac2.chr10(-):89144112-89144181|rheMac2_0
  GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
  &gt;mm8.chr2(+):173910832-173910893|mm8_0
  AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------
  &gt;canFam2.chr24(+):46551822-46551889|canFam2_0
  CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C

  &gt;hg18.chr20(+):56827443-56827480|hg18_1
  ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
  &gt;panTro2.chr20(+):56528760-56528797|panTro2_1
  ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
  &gt;rheMac2.chr10(-):89144181-89144218|rheMac2_1
  ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG

-----

**Example 2b**: Multiple Block Approach **Include hg18 and mm8** and **exclude blocks with missing species**:

The following alignment::

  ##maf version=1
  a score=68686.000000
  s hg18.chr20     56827368 75 +  62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 
  s panTro2.chr20  56528685 75 +  62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 
  s rheMac2.chr10  89144112 69 -  94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA------- 
  s mm8.chr2      173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- 
  s canFam2.chr24  46551822 67 +  50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C 

  a score=10289.000000
  s hg18.chr20    56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 
  s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 
  s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG 

will be converted to (**note** that the second MAF block, which does not have mm8, is not included in the output)::

  &gt;hg18.chr20(+):56827368-56827443|hg18_0
  GACAGGGTGCATCTGGGAGGGCCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC
  &gt;mm8.chr2(+):173910832-173910893|mm8_0
  AGAAGGATCCACCT---------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------

------

.. class:: infomark

**About formats**

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

 - The .maf format is line-oriented. Each multiple alignment ends with a blank line.
 - Each sequence in an alignment is on a single line.
 - Lines starting with # are considered to be comments.
 - 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.
 - Some MAF files may contain two optional line types: 

   - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line; 
   - An "e" line containing information about the size of the gap between the alignments that span the current block.


  </help>
</tool>