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Initial commit.

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# =====================================================
# $Id: FastaStats.xml 90 2011-01-19 13:20:31Z [e-mail] $
# $URL: https://trac.nbic.nl/svn/galaxytools/trunk/tools/general/FastaTools/FastaStats.xml $
# $LastChangedDate: 2011-01-19 07:20:31 -0600 (Wed, 19 Jan 2011) $ 
# $LastChangedRevision: 90 $
# $LastChangedBy: [e-mail] $
# =====================================================
-->
<tool id="FastaStats1" name="FastaStats">
  <description>List statistics for sequences in a FASTA file</description>
  <command interpreter="perl">FastaStats.pl $get_positional_composition_stats -i $input -o $output -l WARN</command>
  <inputs>
    <param format="fasta" name="input" type="data" label="FASTA sequences"/>
    <param name="get_positional_composition_stats" type="boolean" truevalue="-p" falsevalue="" optional="true" label="Calculate positional acid frequencies"/>
  </inputs>
  <outputs>
    <data format="txt" name="output" label="FASTA Statistics for ${input.name}"/>
  </outputs>
  <tests>
    <test>
      <param name="input"       value="fasta_2_proteins.fasta" ftype="fasta"/>
      <output name="output"     file="FastaStats_example_output.txt"/>
    </test>
  </tests>
  <help>

.. class:: infomark

**What it does**

This tool analyzes a collection of sequences in FASTA format and reports: \

 - The total number of sequences.
 - The total number of nucleotide or amino acids.
 - The total frequency of nucleotide or amino acids.
 - The positional frequency of nucleotide or amino acids (optional).
 
-----

**Example**

If the FASTA sequence collection contains these two sequences::

	&gt;UniProtKB:Q42593 L-ascorbate peroxidase T, chloroplastic;
	MSVSLSAASHLLCSSTRVSLSPAVTSSSSSPVVALSSSTSPHSLGSVASSSLFPHSSFVL
	QKKHPINGTSTRMISPKCAASDAAQLISAKEDIKVLLRTKFCHPILVRLGWHDAGTYNKN
	IEEWPLRGGANGSLRFEAELKHAANAGLLNALKLIQPLKDKYPNISYADLFQLASATAIE
	EAGGPDIPMKYGRVDVVAPEQCPEEGRLPDAGPPSPADHLRDVFYRMGLDDKEIVALSGA
	HTLGRARPDRSGWGKPETKYTKTGPGEAGGQSWTVKWLKFDNSYFKDIKEKRDDDLLVLP
	TDAALFEDPSFKNYAEKYAEDVAAFFKDYAEAHAKLSNLGAKFDPPEGIVIENVPEKFVA
	AKYSTGKKELSDSMKKKIRAEYEAIGGSPDKPLPTNYFLNIIIAIGVLVLLSTLFGGNNN
	SDFSGF
	&gt;UniProtKB:A0MQ79 Ascorbate peroxidase;
	MVKNYPVVSEEYLIAVDKAKKKLRGFIAEKNCAPLMLRLAWHSAGTFDQCSRTGGPFGTM
	RFKAEQAHSANNGIDIAIRLLEPIKEQFPILSYADFYQLAGVVAVEVTGGPEVPFHPGRP
	DKEEPPVEGRLPDAYKGSDHLRDVFIKQMGLSDQDIVALSGGHTLGRCHKERSGFEGPWT
	ENPLIFDNSYFKELVCGERDGLLQLPSDKALLADPVFHPLVEKYAADEDAFFADYAEAHL
	KLSELGFADA

The reported stats (without optional positional acid frequencies) will be this::
   
	Sequences	2
	Acid A		69
	Acid C		8
	Acid D		44
	Acid E		44
	Acid F		33
	Acid G		52
	Acid H		18
	Acid I		30
	Acid K		50
	Acid L		67
	Acid M		9
	Acid N		22
	Acid P		46
	Acid Q		13
	Acid R		26
	Acid S		57
	Acid T		23
	Acid V		37
	Acid W		7
	Acid Y		21
	Total acids	676

  </help>
</tool>