Mercurial > repos > cristian > notos
diff CpGoe.xml @ 0:1535ffddeff4 draft
planemo upload commit a7ac27de550a07fd6a3e3ea3fb0de65f3a10a0e6-dirty
author | cristian |
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date | Thu, 07 Sep 2017 08:51:57 -0400 |
parents | |
children | cb8bac9d0d37 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CpGoe.xml Thu Sep 07 08:51:57 2017 -0400 @@ -0,0 +1,57 @@ +<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>