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6
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1 <tool id="getLetterDistribution1" name="Get Letter Distribution">
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15
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2 <description>Calculate distribution for each nucleotide per position for all short reads</description>
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6
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3 <command interpreter="python">
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4 WrappGetLetterDistribution.py -i $inputFileName
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5 #if $formatType.FormatInputFileName == 'fasta':
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6 -f fasta
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7 #else :
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8 -f fastq
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9 #end if
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10 -c $ouputFileNameCSV -a $ouputFileNamePNG1 -b $ouputFileNamePNG2
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11 </command>
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12 <inputs>
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13 <conditional name="formatType">
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14 <param name="FormatInputFileName" type="select" label="Input File Format">
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15 <option value="fasta">fasta</option>
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16 <option value="fastq" selected="true">fastq</option>
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17 </param>
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18 <when value="fasta">
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19 <param name="inputFileName" format="fasta" type="data" label="Fasta Input File"/>
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20 </when>
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21 <when value="fastq">
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22 <param name="inputFileName" format="fastq" type="data" label="Fastq Input File"/>
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23 </when>
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24 </conditional>
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25 </inputs>
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26
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27 <outputs>
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28 <data name="ouputFileNameCSV" format="tabular" label="[getLetterDistribution] CSV File"/>
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29 <data name="ouputFileNamePNG1" format="png" label="[getLetterDistribution] PNG File 1"/>
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30 <data name="ouputFileNamePNG2" format="png" label="[getLetterDistribution] PNG File 2"/>
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15
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="FormatInputFileName" value="fastq" />
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35 <param name="inputFileName" value="short_fastq.fastq" />
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36 <output name="outputFileNameCSV" file="exp_getletterdistribution_short_fastq.csv" />
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37 </test>
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38 </tests>
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39
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40 <help>
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41 The script gets the nucleotide distribution of the input sequence list. It outputs two files. The first file shows the nucleotide distribution of the data. More precisely, a point (*x*, *y*) on the curve **A** shows that *y* sequences have *x*% of **A**.
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42
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43 The second plot shows the average nucleotide distribution for each position of the read. You can use it to detect a bias in the first nucleotides, for instance. A point *x*, *y* on the curve **A** shows that at the position *x*, there are *y*% of **A**. A point (*x*, *y*) on the curve **#** tells you that *y*% of the sequences contain not less than *x* nucleotides. By definition, this latter line is a decreasing function. It usually explains why the tail of the other curves are sometimes erratic: there are few sequences.
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44 </help>
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6
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45 </tool>
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