view faCount.xml @ 17:0847315fa035 draft

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<tool id="faCount" name="faCount">
    <description> Count base statistics and CpGs in FASTA files.</description>
    <requirements>
        <requirement type="package" version="1.0">faCount</requirement>
    </requirements>
    <command>
	faCount $summary $dinuc $strands $input > $output
    </command>

    <inputs>
	<param name="input" type="data" format="fasta" label="FASTA file" />
	<param name="summary" type="boolean" checked="false" falsevalue="" truevalue="-summary" label="Show only summary statistics" />
	<param name="dinuc" type="boolean" checked="false" falsevalue="" truevalue="-dinuc" label="Include statistics on dinucletoide frequencies" />
	<param name="strands" type="boolean" checked="false" falsevalue="" truevalue="-strands" label="Count bases on both strands" />
    </inputs>

    <outputs>
	<data format="tabular" name="output" />
    </outputs>

    <tests>
	<test>
	    <param name="input" value="1.fasta" />
	    <output name="output" file="2.tabular" />
	</test>
	<test>
	    <param name="input" value="1.fasta" />
	    <param name="summary" value="true" />
	    <param name="dinuc" value="true" />
	    <param name="strands" value="true" />
	    <output name="output" file="3.tabular" />
    	</test>
    </tests>

    <help>
**What it does**

faCount_ - Count base statistics and CpGs in FA files.

.. _faCount: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faCount

**Usage**
  
faCount file(s).fa -summary -dinuc -strands

**Examples**

Example 1::

  faCount 1.fasta

  #seq		len	A	C	G	T	N	cpg
  HSFAU1	515	125	138	146	106	0	23
  HSFAU2	514	124	138	146	106	0	25
  HSFAU3	518	125	139	149	105	0	25
  HSFAU4	524	128	142	148	106	0	26
  HSFAU5	518	124	138	147	109	0	25
  total		2589	626	695	736	532	0	124

Example 2::

  faCount 1.fasta -summary

  #seq		len	A	C	G	T	N	cpg
  total		2589	626	695	736	532	0	124
  prcnt		1.0  	0.2418	0.2684	0.2843	0.2055	0.0000	0.0479

Example 3::

  faCount 1.fasta -summary -strands
  
  #seq		len	A	C	G	T	N	cpg
  total		5178	1158	1431	1431	1158	0	248
  prcnt		1.0  	0.2236	0.2764	0.2764	0.2236	0.0000	0.0479

    </help>

</tool>