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author | cristian |
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date | Thu, 07 Sep 2017 08:51:57 -0400 |
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<tool id="CpGoe" name="Calculate CpNo/e" version="1.0.0"> <requirements> <requirement type="package" version="5.8.0">perl</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command><![CDATA[ perl ${__tool_directory__}/CpGoe.pl -f $fastafile -a $algo -c $context -o $outfile -m $minlength ]]></command> <inputs> <param name="fastafile" type="data" format="fasta" /> <param name="context" type="select" label="Select context to calculate the CpNo/e ratio" > <option value="CpG" selected="selected">CpG</option> <option value="CpA">CpA</option> <option value="CpC">CpC</option> <option value="CpT">CpT</option> </param> <param name="algo" type="select" label="Select algorithm to calculate the CpGo/e ratio" > <option value="1">(CpG / (C * G)) * (L^2 / L-1)</option> <option value="2">Gardiner-Garden and Frommer (CpG / (G + C))*L</option> <option value="3">Zeng and Yi (CpG / L) / ((C + G)/L)^2</option> <option value="4">Saxonov, Berg and Brutlag CpG / ((C + G)/2)^2</option> </param> <param name="minlength" type="integer" value="200" help="Minimum length of the sequence to calculate CpGo/e ratio" /> </inputs> <outputs> <data name="outfile" format="tabular" /> </outputs> <tests> <test> <param name="fastafile" value="9_seqs.fa"/> <output name="outfile1" file="9_seqs_cpgoe.csv"/> </test> </tests> <help><![CDATA[ CpGoe.pl -f fasta-file -a algo -c context -o output_file -m minlength Reads multi fasta files, writes name, length, CpGs and GpCs, CpGo/e ratios and other quantities into TAB file for each sequence. The available contexts (-c) are CpG, CpA, CpC, CpT. Default CpG. The algorithms (-a) available for -a are the following:: 1 => (CpG / (C * G)) * (L^2 / L-1) 2 => (CpG / (C * G)) * L 3 => (CpG / L) / ((C + G) / L)^2 4 => (CpG / (C + G)/2)^2 Where L represents the length of the sequence, CpG represents the count of CG dinucleotide, C and G represent the count for the respective bases and TG represents the number of TG dinucleotides. ]]></help> <citations> <citation> <citation type="doi">10.1101/180463</citation> </citation> </citations> </tool>