root/galaxy-central/tools/regVariation/compute_motifs_frequency.xml @ 2

<tool id="compute_motifs_frequency" name="Compute Motif Frequencies" version="1.0.0">
  <description>in indel flanking regions</description>
  
  
  <command interpreter="perl">
    compute_motifs_frequency.pl $inputFile1 $inputFile2 $inputNumber3 $outputFile1 $outputFile2
  </command>
  
  
  <inputs>
 
    <param format="tabular" name="inputFile1" type="data" label="Select motifs file"/>

    <param format="tabular" name="inputFile2" type="data" label="Select indel flanking regions file from your history"/>
      
    <param type="integer" name="inputNumber3" size="5" value="0" label="What is the size of each window?" help="'0' = all the upstream flanking sequence will be one window only, and the same for the downstream flanking sequence."/>
        
  </inputs>
  
  
  <outputs>
    <data format="tabular" name="outputFile1"/>
    <data format="tabular" name="outputFile2"/>
  </outputs>
  
  <tests>
        <test>
                <param name="inputFile1" value="motifs1.tabular" />
                <param name="inputFile2" value="indelsFlankingSequences1.tabular" />
        <param name="inputNumber3" value="0" />
        <output name="outputFile1" file="flankingSequencesWindows0.tabular" />
        <output name="outputFile2" file="motifFrequencies0.tabular" />    
        </test>
        
        <test>
                <param name="inputFile1" value="motifs1.tabular" />
                <param name="inputFile2" value="indelsFlankingSequences1.tabular" />
        <param name="inputNumber3" value="10" />
        <output name="outputFile1" file="flankingSequencesWindows10.tabular" /> 
        <output name="outputFile2" file="motifFrequencies10.tabular" />    
        </test>
  </tests>

   
   <help>

.. class:: infomark

**What it does**

This program computes the frequency of motifs in the flanking regions of indels found in a chromosome or a genome.
Each indel has an upstream flanking sequence and a downstream flanking one. Each of the upstream and downstream flanking 
sequences will be divided into a certain number of windows according to the window size input by the user. 
The frequency of a motif in a certain window in one of the two flanking sequences is the total sum of occurrences of 
that motif in that window of that flanking sequence over all indels. The indel flanking regions file will be taken
from your history or it will be uploaded, whereas the motifs file should be uploaded.

- The first input file is the motifs file and it is a tabular file consisting of two columns:

 - the first column represents the motif name
 - the second column represents the motif sequence, as follows::
  
        dnaPolPauseFrameshift1  GAG
        dnaPolPauseFrameshift2  ACG
        xSites1                 CCG

- The second input file is the indels flanking regions file and it is a tabular file consisting of five columns:

 - the first column represents the indel start coordinate
 - the second column represents the indel end coordinate
 - the third column represents the indel length
 - the fourth column represents the upstream flanking sequence
 - the fifth column represents the upstream flanking sequence, as follows::
  
        16694766   16694768   3   GTGGGTCCTGCCCAGCCTCTGCCTCAGAGGGAAGAGTAGAGAACTGGG   AGAGCAGGTCCTTAGGGAGCCCGAGGAAGTCCCTGACGCCAGCTGTTCTCGCGGACGAA
        25169542   25169545   4   caagcccacaagccttcagaccatagcaCGGGCTCCAGAGGTGTGAGG   CAGGTCAGGTGCTTTAGAAGTCAAAAACTCTCAGTAAGGCAAATCACCCCCTATCTCCT
        41929580   41929585   6   ggctgtcgtatggaatctggggctcaggactctgtcccatttctctaa   accattctgcTTCAACCCAGACACTGACTGTTTTCCAAATTTACTTGTTTGTTTGTTTT


-----

.. class:: warningmark

**Notes**

- The lengths of the upstream flanking sequences must be equal for all indels.
- The lengths of the downstream flanking sequences must be equal for all indels.
- If the length of the upstream flanking sequence L is not an integer multiple of the window size S, in other words if L/S = m + r where m is the result of division and r is the remainder, then the upstream flanking sequence will be divided into m windows only starting from the indel, and the rest of the sequence will not be considered. The same rule applies to the downstream flanking sequence. 

-----

The **output** of this program is two files:

- The first output file is a tabular file and represents the windows of both upstream  and downstream flanking sequences. It consists of multiple left columns representing the windows of the upstream flanking sequence, followed by one column representing the indels, then followed by multiple right columns representing the windows of the downstream flanking sequence, as follows::

        cgaggtcagg      agatcgagac      catcctggct      aacatggtga      aatcccgtct      ctactaaaaa      indel   aaatttatat      ttataaacaa      ttttaataca      cctatgttta      ttatacattt
        GCCAGTTTAT      GGTCTAACAA      GGAGAGAAAC      AGGGGGCTGA      AGGGGTTTCT      TAACCTCCAG      indel   TTCCGGGCTC      TGTCCCTAAC      CCCCAGCTAG      GTAAGTGGCA      AAGCACTTCT
        CAGTGGGACC      AAGCACTGAA      CCACTTTGGG      GAGAATCTCA      CACTGGGGCC      CTCTGACACC      indel   tatatatttt      tttttttttt      tttttttttt      tttttttttg      agatggtgtc
        AGAGCAGCAG      CACCCACTTT      TGCAGTGTGT      GACGTTGGTG      GAGCCATCGA      AGTCTGTGCT      indel   GAGCCCTCCC      CAGTGCTCCG      AGGAGCTGCT      GTTCCCCCTG      GAGCTCAGAA

- The second output file is a tabular file and represents the motif frequencies in every window of every flanking sequence. The first column on the left represents the names of motifs. The other columns represent the frequencies of motifs in the windows that correspond to the ones in the first output file, as follows::

        dnaPolPauseFrameshift1  2       3       1       0       1       2       indel   0       2       2       1       3
        dnaPolPauseFrameshift2  2       3       1       0       1       2       indel   0       2       2       1       3
        xSites1                 3       2       0       1       1       2       indel   1       1       3       2       3
        
  </help>
   
</tool>