Mercurial > repos > devteam > fastq_quality_boxplot
diff fastq_quality_boxplot.xml @ 2:3987db70a4b0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
| author | iuc |
|---|---|
| date | Tue, 08 May 2018 13:26:13 -0400 |
| parents | f95284aa2946 |
| children | 7cf5b1d072b5 |
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--- a/fastq_quality_boxplot.xml Mon Jul 21 15:11:49 2014 -0400 +++ b/fastq_quality_boxplot.xml Tue May 08 13:26:13 2018 -0400 @@ -1,19 +1,32 @@ -<tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="1.0.0"> - <description></description> - <requirements> - <requirement type="package" version="0.0.13">fastx_toolkit</requirement> - </requirements> - <command>fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o $output</command> - - <inputs> - <param format="txt" name="input" type="data" label="Statistics report file" help="output of 'FASTQ Statistics' tool" /> - </inputs> +<tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="1.0.1"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +#import re +#set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($input.element_identifier)) +fastq_quality_boxplot_graph.sh +-t '$escaped_element_identifier' +-i '$input' +-o '$output' + ]]></command> - <outputs> - <data format="png" name="output" metadata_source="input" /> - </outputs> -<help> + <inputs> + <param name="input" type="data" format="txt" label="Statistics report file" help="output of 'FASTQ Statistics' tool" /> + </inputs> + <outputs> + <data name="output" format="png" metadata_source="input" /> + </outputs> + <tests> + <test> + <param name="input" value="fastq_quality_boxplot-in1.fastq" /> + <output name="output" file="fastq_quality_boxplot-out1.png" compare="sim_size" delta="768" /> + </test> + </tests> + <help><![CDATA[ **What it does** Creates a boxplot graph for the quality scores in the library. @@ -49,9 +62,7 @@ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ - - - -</help> + ]]></help> + <expand macro="citations" /> <!-- FASTQ-Quality-Boxplot is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> </tool>