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planemo upload for repository https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ commit 3c77e032f5e4a3ec4bf3828e5179d7a598d8a006
author | iuc |
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date | Fri, 30 Sep 2022 17:50:57 +0000 |
parents | f14a21f3d5b1 |
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<?xml version="1.0"?> <tool id="seqcomplexity" name="Calculate sequence complexity" version="@TOOL_VERSION@" profile="21.05"> <description>total and per read</description> <macros> <token name="@TOOL_VERSION@">0.1.2</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">seqcomplexity</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ seqcomplexity --fastq '$input_fastq' > '$output_json' ]]></command> <inputs> <param name="input_fastq" type="data" format="fastq" label="Input reads in FASTQ format"/> </inputs> <outputs> <data name="output_json" format="json"/> </outputs> <tests> <test> <param name="input_fastq" value="example.fastqsanger"/> <output name="output_json"> <assert_contents> <has_text_matching expression="complexity"/> </assert_contents> </output> </test> <test> <param name="input_fastq" value="example.fastq.gz"/> <output name="output_json"> <assert_contents> <has_text_matching expression="complexity"/> </assert_contents> </output> </test> <test> <param name="input_fastq" value="example.fastq.notgzextension"/> <output name="output_json"> <assert_contents> <has_text_matching expression="complexity"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ Calculates Per-Read and Total Sequence Complexity from FastQ file. Complexity is the number of base pairs of unique or nonrepeating DNA in a given segment of DNA, or component of the genome. ]]></help> <citations> </citations> </tool>