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author swebb
date Thu, 20 Jun 2013 12:13:43 -0400
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<tool id="pyAlignment2Tab" name="pyAlignment2Tab">
	  <description>converter</description>
	  <requirements>
        	<requirement type="package">pyCRAC</requirement>
    	  </requirements>
 	  <command interpreter="python">/usr/local/bin/pyAlignment2Tab.py -f $input --limit $limit -o $output --singlefile
 	  </command>
	  <version_command>/usr/local/bin/pyAlignment2Tab.py --version</version_command>
 	  <inputs>
	      	<param name="input" type="data" format="fasta" label="pyReadAligner output file -f" help="Fasta file"/>
	      	<param name="limit" type="integer" format="integer" value="90" size="4" label="Set the column width of alignment" help="Enter a value > 50">
			<validator type="in_range" min="50" message="Please enter a value greater than 50"/>
	      	</param>
		<param name="label" type="text" format="txt" size="30" value="pyAlignment2Tab" label="Enter output file label -o" />
 	  </inputs>
 	  <outputs>
	    	<data name="output" format="txt" label="${label.value}.tab"/>
 	  </outputs>
	  <help>

.. class:: infomark

**pyAlignment2Tab**

pyAlignment2Tab is part of the pyCRAC_ package. Converts pyReadAligner fasta output to a tabular alignment output.

Example::

    The tool expects a standard pyReadAligner fasta-formatted output file:
    
        >GeneX
        ATGTCTCGTACTAACATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCACCACAGAGTGCTACTGCAAATAGCAGGAGCAGCAACAGCAGCAGCGAGAGTAGTAGTAACAAAAACAATATCAATGTCGGCGTCGGTGACGATAGCGGTAA
        >257930-10
        ---TCTCGTACcAACATGGATACAAGACACGCACATTCTGCTT----------------------------------------------------------------------------------------------------------------
        >3664964-1
        ---TCTCGcACcAACATGGATACAAGACACGCACATTtTGCTT----------------------------------------------------------------------------------------------------------------
        >4033560-1
        ---TCTCGTACcAACATGGATACAAGACACGCACATTCTGtTT----------------------------------------------------------------------------------------------------------------
        >8571880-1
        ---TCTCGTACcAACATGGATACAAGACACGCAgATTCTGCTT----------------------------------------------------------------------------------------------------------------
        >9617396-1
        ---TCTCGTACcAACATGGATACAAGACACGCcCATTCTGCTT----------------------------------------------------------------------------------------------------------------
        >843368-5
        ------------AACAcGGATACAAGACACGCACATTCTG-------------------------------------------------------------------------------------------------------------------
        >854553-5
        ------------AACATGGATACAAGACACGCAC--TCTG-------------------------------------------------------------------------------------------------------------------
        >1522401-2
        --------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgA-----------------------------------------------------------------------------------------------------
        >5981234-1
        --------------CATGGATACAAGACACGCACAcTCTGCTTTACTGGCAGCA-----------------------------------------------------------------------------------------------------
        >997684-4
        --------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCA-----------------------------------------------------------------------------------------------------
        >1046653-4
        ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgAC----------------------------------------------------------------------------------------------------
        >1103730-4
        ---------------ATGGATACAAGACACGCACAcTCTG-------------------------------------------------------------------------------------------------------------------
        >1603913-2
        ---------------ATGGATACAAGAaACGCACAcTCTG-------------------------------------------------------------------------------------------------------------------
        >180349-12
        ---------------ATGGATACAAGACACGCACATTCcGCTTTACTG-----------------------------------------------------------------------------------------------------------
        >1985106-1
        ---------------ATGGATACAAGACACGCACATTCgGCTTTACTGGCAGCcC----------------------------------------------------------------------------------------------------
        >1987775-1
        ---------------ATGGATACccGACACGCACATTCTGCTTTACTGcCAGCAC----------------------------------------------------------------------------------------------------
        >2258725-1
        ---------------ATGGATACAAGACACGCACATTCTGCTTTgCTGGCAGCAC----------------------------------------------------------------------------------------------------
        >2631987-1
        ---------------ATGGATACAAGACACGCACATTCTGCTTTACcGGCAGgAC----------------------------------------------------------------------------------------------------

    This will be converted into:
    
                1	.........|.........|.........|.........|.........|.........|.........|.........|.........| 90
        >GeneX          ATGTCTCGTACTAACATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCACCACAGAGTGCTACTGCAAATAGCAGGAGCAGCAAC
        >257930-10	---TCTCGTACcAACATGGATACAAGACACGCACATTCTGCTT-----------------------------------------------
        >3664964-1	---TCTCGcACcAACATGGATACAAGACACGCACATTtTGCTT-----------------------------------------------
        >4033560-1	---TCTCGTACcAACATGGATACAAGACACGCACATTCTGtTT-----------------------------------------------
        >8571880-1	---TCTCGTACcAACATGGATACAAGACACGCAgATTCTGCTT-----------------------------------------------
        >9617396-1	---TCTCGTACcAACATGGATACAAGACACGCcCATTCTGCTT-----------------------------------------------
        >843368-5	------------AACAcGGATACAAGACACGCACATTCTG--------------------------------------------------
        >854553-5	------------AACATGGATACAAGACACGCAC--TCTG--------------------------------------------------
        >1522401-2	--------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgA------------------------------------
        >5981234-1	--------------CATGGATACAAGACACGCACAcTCTGCTTTACTGGCAGCA------------------------------------
        >997684-4	--------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCA------------------------------------
        >1046653-4	---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgAC-----------------------------------
        >1103730-4	---------------ATGGATACAAGACACGCACAcTCTG--------------------------------------------------
        >1603913-2	---------------ATGGATACAAGAaACGCACAcTCTG--------------------------------------------------
        >180349-12	---------------ATGGATACAAGACACGCACATTCcGCTTTACTG------------------------------------------
        >1985106-1	---------------ATGGATACAAGACACGCACATTCgGCTTTACTGGCAGCcC-----------------------------------
        >1987775-1	---------------ATGGATACccGACACGCACATTCTGCTTTACTGcCAGCAC-----------------------------------
        >2258725-1	---------------ATGGATACAAGACACGCACATTCTGCTTTgCTGGCAGCAC-----------------------------------
        >2631987-1	---------------ATGGATACAAGACACGCACATTCTGCTTTACcGGCAGgAC-----------------------------------
        >337206-9	---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCAC-----------------------------------
        >4616761-1	---------------ATGGATAgAAGACACGCACATTCTGCTTTACTGGtAGCAC-----------------------------------
        >4756312-1	---------------ATGGATACAAcACACGCACAcTCTG--------------------------------------------------
        >4763682-1	---------------ATGGATACAAGACACGCACATTCcGCTTTcCTG------------------------------------------
        >5971268-1	---------------ATGGATACAAGACACGCACATTCcGCTcTACTc------------------------------------------
        >6644790-1	---------------ATGGATACAAGACACGCACATTCTGCTTTACTcGCAGCAC-----------------------------------
        >7112423-1	---------------ATGGATACAAGACACGCACATTCTGCTTTACTGtCAGCAC-----------------------------------
        >7559990-1	---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCcGgAC-----------------------------------
        >8007281-1	---------------ATGGATAtAAGACACGCACAcTCTG--------------------------------------------------
        >9150255-1	---------------ATGGATACAcGACACGCACATTCcGCTTTcCTG------------------------------------------
        >9180814-1	---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgcC-----------------------------------
        >963117-4	---------------ATGGATACAAGACACGCACATTCTGCTTTACcGGCAGCAC-----------------------------------
        >9672073-1	---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCcC-----------------------------------
        >971218-4	---------------ATGGATACAAGACACGCACATcCTGCTTTACTGG-AGCACC----------------------------------
        >10040274-1	-------------------ATACAAGACACGCACATTCTGCTTTACTGGCAGgACCACA-------------------------------
        >1063072-4	-------------------ATACAAGACACGCACATTCTGCTTcACTGGCAGCACCACA-------------------------------
        >1430188-2	-------------------ATACAAGACACGCACATTCTGCTTTACTGGCAGCACCACA-------------------------------
        >5196741-1	-------------------ATACAAGACACGCACATTCTGCTTcACTGGCcGCACCACA-------------------------------
        >6017337-1	-------------------ATACAAGACACGCACATTCTGCTTcACTGtCAGaACCcCA-------------------------------
        >7159053-1	-------------------ATACAAGACACGCACATTCTGCTTTACTGGCAGCACCcaA-------------------------------
        >7528336-1	-------------------ATACAAGACACGCACATTCTGCTTcACTGGCAGCAaCACA-------------------------------
        >735584-6	--------------------------------------------------------ACAGAGTGCTACTGCAAAcAGCAGGAGCAGCAAC
        >8551047-1	--------------------------------------------------------ACAGAGTGCTAtTGCAAAcAGCAGGAGtAGtAAC
        >3000121-1	------------------------------------------------------------AGTcCTACcGCAAATAGCAGcAGCAGCAAC
        >928481-5	------------------------------------------------------------AGTGCTACcGCAAATAGCAGGAGCAGCAAC
        >126987-15	----------------------------------------------------------------------CAAATAGCAGGAGCAGCAAC
        >3122797-1	----------------------------------------------------------------------CAAATAGCAGGcGCAGCAAC
        >6684686-1	----------------------------------------------------------------------CAAATAGCAGGAGCAGCAAC
    
        Note that the column width here was set to 90 characters
   
.. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
        
------

**Parameter list**

Options::

  	-f data.fasta   
                        Type the path to the fasta file that you want to use.
  	--limit=90     
                        Allows the user to set the column width of the alignment. Default=90 characters
	-o output.fasta 
                        Provide the name of your output file
		
 	</help>
</tool>