| Next changeset 1:63d6e2daad48 (2013-12-03) |
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Commit message:
Uploaded tool tarball. |
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added:
fastx_nucleotides_distribution.xml tool_dependencies.xml |
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| diff -r 000000000000 -r bcc5424a4a3c fastx_nucleotides_distribution.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastx_nucleotides_distribution.xml Wed Sep 25 11:14:24 2013 -0400 |
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| @@ -0,0 +1,53 @@ +<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" version="1.0.0" name="input" type="data" label="Statistics Text File" help="output of 'FASTX Statistics' tool" /> + </inputs> + + <outputs> + <data format="png" version="1.0.0" 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_path}/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_path}/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_path}/fastx_icons/fastq_nucleotides_distribution_3.png + +But most of the time, the chart will look rather random: + +.. image:: ${static_path}/fastx_icons/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> |
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| diff -r 000000000000 -r bcc5424a4a3c tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 25 11:14:24 2013 -0400 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="fastx_toolkit" version="0.0.13"> + <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |