Mercurial > repos > devteam > fastx_nucleotides_distribution
view fastx_nucleotides_distribution.xml @ 5:ad116ae3f4d9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
author | iuc |
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date | Thu, 30 Jan 2020 13:30:27 -0500 |
parents | 21796f46e0ba |
children | b6b54ba71bd8 |
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<tool id="cshl_fastx_nucleotides_distribution" version="1.0.1" name="Draw nucleotides distribution chart"> <description></description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ fastx_nucleotide_distribution_graph.sh -t '$input.name' -i '$input' -o '$output' ]]></command> <inputs> <param name="input" type="data" format="txt" label="Statistics text file" help="Output of 'FASTX Statistics' tool" /> </inputs> <outputs> <data name="output" format="png" metadata_source="input" /> </outputs> <tests> <test> <param name="input" value="fastx_nucleotides_distribution-in1.txt" /> <output name="output" file="fastx_nucleotides_distribution-out1.png" compare="sim_size" delta="4000" /> </test> </tests> <help><![CDATA[ **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> <expand macro="citations" /> <!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> </tool>