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author bjoern-gruening
date Wed, 11 Jan 2012 09:34:45 -0500
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<tool id="glimmer3-build-icm" name="glimmer3-build-icm" version="0.1">
  <description>glimmer3-build-icm</description>
  <command> tigr-glimmer build-icm -r  $output &lt; $inputfile  </command>
  <inputs>
	<param name="inputfile" type="data" format="txt" label="Dataset" help="Dataset missing? See TIP below"/>
  </inputs>
  <outputs>
    <data format="icm" name="output" />
  </outputs>
  <tests>
	<test>
		<param name="inputfile" value='glimmer3/seqTest.fa'/>
		<output name="output" file='glimmer3/buildICMTestOutput.dat'/>
	</test>	
 </tests>

<help>

**What it does**

	This program constructs an interpolated context model (ICM) from an input set of sequences.

-----

**Glimmer Overview**

::

**************		**************		**************		**************		
*            *		*	     *		*            *		*            *
* long-orfs  *  ===>	*   Extract  *	===>	* build-icm  *  ===>	*  glimmer3  *	
*            *		*	     *		*	     *  	*	     *	
**************		**************		**************		**************

-----

**Example**

* input::

	-Genome Sequence

	>CELF22B7  C.aenorhabditis elegans (Bristol N2) cosmid F22B7
	GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
	GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
	TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
	TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
	GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
	ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
	AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
	CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA
	TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC
	AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA
	GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC
	AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC
	CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA
	AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC
	GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT
	.....

* output:
	interpolated context model (ICM) 


-------

**References**

A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007).


 </help>

</tool>