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comparison fastx_toolkit-0.0.6/galaxy/tools/fastx_toolkit/fastx_nucleotides_distribution.xml @ 3:997f5136985f draft default tip

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author xilinxu
date Thu, 14 Aug 2014 04:52:17 -0400
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1 <tool id="cshl_fastx_nucleotides_distribution" name="Nucleotides Distribution">
2 <description>chart</description>
3 <command>fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output</command>
4
5 <inputs>
6 <param format="txt" name="input" type="data" label="Statistics Text File (output of 'FASTX Statistics' tool)" />
7 </inputs>
8
9 <outputs>
10 <data format="png" name="output" metadata_source="input" />
11 </outputs>
12 <help>
13
14 **What it does**
15
16 Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library.
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18 .. class:: infomark
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20 **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
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22 -----
23
24 **Output Examples**
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28 The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT**
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30 .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_1.png
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38 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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40 .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_2.png
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49 The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem):
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51 .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_3.png
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60 But most of the time, the chart will look rather random:
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62 .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_4.png
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64 </help>
65 </tool>
66 <!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->