Mercurial > repos > devteam > fastx_nucleotides_distribution
view fastx_nucleotides_distribution.xml @ 3:18a51655db17 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:39:18 -0500 |
parents | 9353010b95df |
children | 21796f46e0ba |
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<tool id="cshl_fastx_nucleotides_distribution" version="1.0.0" name="Draw nucleotides distribution chart"> <description></description> <requirements> <requirement type="package" version="0.0.13">fastx_toolkit</requirement> </requirements> <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:: 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:: 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:: fastq_nucleotides_distribution_3.png But most of the time, the chart will look rather random: .. image:: fastq_nucleotides_distribution_4.png ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ </help> <!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> </tool>