annotate CpGoe.xml @ 1:cb8bac9d0d37 draft default tip

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author cristian
date Thu, 07 Sep 2017 10:21:45 -0400
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1 <tool id="CpGoe" name="Calculate CpNo/e" version="1.0.0">
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2 <requirements>
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3 <requirement type="package" version="5.8.0">perl</requirement>
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4 </requirements>
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5 <stdio>
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6 <exit_code range="1:" />
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7 </stdio>
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8 <command><![CDATA[
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9 perl ${__tool_directory__}/CpGoe.pl -f $fastafile -a $algo -c $context -o $outfile -m $minlength
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10 ]]></command>
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11 <inputs>
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12 <param name="fastafile" type="data" format="fasta" />
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13 <param name="context" type="select" label="Select context to calculate the CpNo/e ratio" >
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14 <option value="CpG" selected="selected">CpG</option>
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15 <option value="CpA">CpA</option>
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16 <option value="CpC">CpC</option>
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17 <option value="CpT">CpT</option>
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18 </param>
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19 <param name="algo" type="select" label="Select algorithm to calculate the CpGo/e ratio" >
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20 <option value="1">(CpG / (C * G)) * (L^2 / L-1)</option>
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21 <option value="2">Gardiner-Garden and Frommer (CpG / (G + C))*L</option>
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22 <option value="3">Zeng and Yi (CpG / L) / ((C + G)/L)^2</option>
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23 <option value="4">Saxonov, Berg and Brutlag CpG / ((C + G)/2)^2</option>
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24 </param>
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25 <param name="minlength" type="integer" value="200" help="Minimum length of the sequence to calculate CpGo/e ratio" />
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26 </inputs>
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27 <outputs>
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28 <data name="outfile" format="tabular" />
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="fastafile" value="9_seqs.fa"/>
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33 <output name="outfile1" file="9_seqs_cpgoe.csv"/>
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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37 CpGoe.pl -f fasta-file -a algo -c context -o output_file -m minlength
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38
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39 Reads multi fasta files, writes name, length, CpGs and GpCs, CpGo/e ratios and other quantities into TAB file for each sequence.
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40
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41 The available contexts (-c) are CpG, CpA, CpC, CpT. Default CpG.
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42
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43 The algorithms (-a) available for -a are the following::
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44
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45 1 => (CpG / (C * G)) * (L^2 / L-1)
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46 2 => (CpG / (C * G)) * L
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47 3 => (CpG / L) / ((C + G) / L)^2
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48 4 => (CpG / (C + G)/2)^2
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49
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50 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.
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51 ]]></help>
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52 <citations>
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53 <citation type="doi">10.1101/180463</citation>
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54 </citations>
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55 </tool>