view seqcomplexity.xml @ 1:054c3355458d draft default tip

planemo upload for repository https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ commit 3c77e032f5e4a3ec4bf3828e5179d7a598d8a006

<?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>