Mercurial > repos > devteam > fastx_nucleotides_distribution
diff fastx_nucleotides_distribution.xml @ 3:3b6c41fc2d21 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
| author | iuc |
|---|---|
| date | Tue, 08 May 2018 12:51:52 -0400 |
| parents | 05f35740cd79 |
| children | 67e441bc4265 |
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--- a/fastx_nucleotides_distribution.xml Tue Jun 03 15:07:52 2014 -0400 +++ b/fastx_nucleotides_distribution.xml Tue May 08 12:51:52 2018 -0400 @@ -1,19 +1,28 @@ -<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 $output</command> - - <inputs> - <param format="txt" name="input" type="data" label="Statistics Text File" help="output of 'FASTX Statistics' tool" /> - </inputs> - - <outputs> - <data format="png" name="output" metadata_source="input" /> - </outputs> -<help> - +<tool id="cshl_fastx_nucleotides_distribution" version="1.0.1" name="Draw nucleotides distribution chart"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +fastx_nucleotide_distribution_graph.sh +-t '$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="512" /> + </test> + </tests> + <help><![CDATA[ **What it does** Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library. @@ -29,7 +38,7 @@ 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 @@ -47,7 +56,7 @@ 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) --> + ]]></help> + <expand macro="citations" /> + <!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> </tool>