Mercurial > repos > nikos > ucsc_tools
changeset 13:5d07b82fef18 draft
Uploaded
author | nikos |
---|---|
date | Tue, 09 Sep 2014 08:53:05 -0400 |
parents | 57823dcd0795 |
children | 12820616d67f |
files | faCount.xml |
diffstat | 1 files changed, 78 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/faCount.xml Tue Sep 09 08:53:05 2014 -0400 @@ -0,0 +1,78 @@ +<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>