diff fastx_nucleotides_distribution.xml @ 0:78a7d28f2a15 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastx_nucleotides_distribution.xml	Wed Jul 10 06:13:48 2013 -0400
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+<tool id="cshl_fastx_nucleotides_distribution" name="Draw nucleotides distribution chart">
+	<description></description>
+	<command>fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o '$output'</command>
+	
+	<inputs>
+		<param format="txt" name="input" type="data" label="Statistics Text File" help="output of 'FASTX Statistics' tool" />
+	</inputs>
+	
+	<outputs>
+		<data format="png" name="output" metadata_source="input"
+		/>
+	</outputs>
+<help>
+
+**What it does**
+
+Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library.
+
+.. class:: infomark
+
+**TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
+
+-----
+
+**Output Examples**
+
+The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT**
+
+.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_1.png
+ 
+In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...**
+
+.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_2.png
+
+The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem):
+
+.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_3.png
+
+But most of the time, the chart will look rather random:
+
+.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_4.png
+
+------
+
+This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+
+ .. __: http://hannonlab.cshl.edu/fastx_toolkit/
+
+</help>
+</tool>
+<!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon ([e-mail]) -->