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annotate seqcomplexity.xml @ 0:a7a4d4b554df draft

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planemo upload for repository https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ commit 44f29b11508c8d407212ef000c16eda0e22922f0
author iuc
date Tue, 07 Jun 2022 09:28:42 +0000
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a7a4d4b554df planemo upload for repository https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ commit 44f29b11508c8d407212ef000c16eda0e22922f0
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1 <?xml version="1.0"?>
a7a4d4b554df planemo upload for repository https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ commit 44f29b11508c8d407212ef000c16eda0e22922f0
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2 <tool id="seqcomplexity" name="Calculate sequence complexity" version="@TOOL_VERSION@" profile="21.05">
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3 <description>total and per read</description>
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4 <macros>
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5 <token name="@TOOL_VERSION@">0.1.0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">seqcomplexity</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 seqcomplexity --fastq '$input_fastq' > '$output_json'
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12 ]]></command>
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13 <inputs>
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14 <param name="input_fastq" type="data" format="fastq" label="Input reads in FASTQ format"/>
a7a4d4b554df planemo upload for repository https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ commit 44f29b11508c8d407212ef000c16eda0e22922f0
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15 </inputs>
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16 <outputs>
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17 <data name="output_json" format="json"/>
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="input_fastq" value="example.fastqsanger"/>
a7a4d4b554df planemo upload for repository https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ commit 44f29b11508c8d407212ef000c16eda0e22922f0
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22 <output name="output_json">
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23 <assert_contents>
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24 <has_text_matching expression="complexity"/>
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25 </assert_contents>
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26 </output>
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27 </test>
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28 <test>
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29 <param name="input_fastq" value="example.fastq.gz"/>
a7a4d4b554df planemo upload for repository https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/ commit 44f29b11508c8d407212ef000c16eda0e22922f0
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30 <output name="output_json">
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31 <assert_contents>
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32 <has_text_matching expression="complexity"/>
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33 </assert_contents>
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34 </output>
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35 </test>
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36 <test>
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37 <param name="input_fastq" value="example.fastq.notgzextension"/>
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38 <output name="output_json">
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39 <assert_contents>
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40 <has_text_matching expression="complexity"/>
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41 </assert_contents>
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42 </output>
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43 </test>
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44 </tests>
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45 <help><![CDATA[
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46 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.
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47 ]]></help>
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48 <citations>
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49 </citations>
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50 </tool>