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1 <tool id="cshl_fastx_nucleotides_distribution" version="1.0.0" name="Draw nucleotides distribution chart">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
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5 </requirements>
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6 <command>fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output</command>
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7
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8 <inputs>
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9 <param format="txt" version="1.0.0" name="input" type="data" label="Statistics Text File" help="output of 'FASTX Statistics' tool" />
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10 </inputs>
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11
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12 <outputs>
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13 <data format="png" version="1.0.0" name="output" metadata_source="input" />
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14 </outputs>
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15 <help>
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16
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17 **What it does**
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18
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19 Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library.
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20
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21 .. class:: infomark
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22
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23 **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
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24
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25 -----
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26
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27 **Output Examples**
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28
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29 The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT**
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30
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31 .. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_1.png
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32
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33 In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...**
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34
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35 .. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_2.png
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36
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37 The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem):
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38
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39 .. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_3.png
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40
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41 But most of the time, the chart will look rather random:
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42
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43 .. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_4.png
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44
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45 ------
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46
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47 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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48
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49 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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50
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51 </help>
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52 <!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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53 </tool>
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