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comparison seqcomplexity.xml @ 0:f14a21f3d5b1 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 09:29:15 +0000
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-1:000000000000 0:f14a21f3d5b1
1 <?xml version="1.0"?>
2 <tool id="seqcomplexity" name="Calculate sequence complexity" version="@TOOL_VERSION@" profile="21.05">
3 <description>total and per read</description>
4 <macros>
5 <token name="@TOOL_VERSION@">0.1.0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">seqcomplexity</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 seqcomplexity --fastq '$input_fastq' > '$output_json'
12 ]]></command>
13 <inputs>
14 <param name="input_fastq" type="data" format="fastq" label="Input reads in FASTQ format"/>
15 </inputs>
16 <outputs>
17 <data name="output_json" format="json"/>
18 </outputs>
19 <tests>
20 <test>
21 <param name="input_fastq" value="example.fastqsanger"/>
22 <output name="output_json">
23 <assert_contents>
24 <has_text_matching expression="complexity"/>
25 </assert_contents>
26 </output>
27 </test>
28 <test>
29 <param name="input_fastq" value="example.fastq.gz"/>
30 <output name="output_json">
31 <assert_contents>
32 <has_text_matching expression="complexity"/>
33 </assert_contents>
34 </output>
35 </test>
36 <test>
37 <param name="input_fastq" value="example.fastq.notgzextension"/>
38 <output name="output_json">
39 <assert_contents>
40 <has_text_matching expression="complexity"/>
41 </assert_contents>
42 </output>
43 </test>
44 </tests>
45 <help><![CDATA[
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.
47 ]]></help>
48 <citations>
49 </citations>
50 </tool>