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1 <tool id="getLetterDistribution1" name="get letter distribution">
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2 <description>Calculate distribution for each nucleotide per position for all short reads</description>
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3 <requirements>
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4 <requirement type="set_environment">PYTHONPATH</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 WrappGetLetterDistribution.py -i $inputFileName
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8 #if $formatType.FormatInputFileName == 'fasta':
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9 -f fasta
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10 #else :
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11 -f fastq
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12 #end if
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13 -c $ouputFileNameCSV -a $ouputFileNamePNG1 -b $ouputFileNamePNG2
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14 </command>
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15 <inputs>
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16 <conditional name="formatType">
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17 <param name="FormatInputFileName" type="select" label="Input File Format">
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18 <option value="fasta">fasta</option>
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19 <option value="fastq" selected="true">fastq</option>
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20 </param>
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21 <when value="fasta">
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22 <param name="inputFileName" format="fasta" type="data" label="Fasta Input File"/>
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23 </when>
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24 <when value="fastq">
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25 <param name="inputFileName" format="fastq" type="data" label="Fastq Input File"/>
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26 </when>
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27 </conditional>
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28 </inputs>
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29
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30 <outputs>
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31 <data name="ouputFileNameCSV" format="tabular" label="[get letter distribution] CSV file"/>
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32 <data name="ouputFileNamePNG1" format="png" label="[get letter distribution] PNG file 1"/>
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33 <data name="ouputFileNamePNG2" format="png" label="[get letter distribution] PNG file 2"/>
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="FormatInputFileName" value="fastq" />
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38 <param name="inputFileName" value="short_fastq.fastq" />
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39 <output name="outputFileNameCSV" file="exp_getletterdistribution_short_fastq.csv" />
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40 </test>
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41 </tests>
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42
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43 <help>
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44 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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45
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46 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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47 </help>
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48 </tool>
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