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author jpayne
date Thu, 27 Jun 2019 13:46:42 -0400
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1 <tool id="shigatyper" name="ShigaTyper" version="1.0.5">
2 <description>Shigella genoserotyping</description>
3 <requirements>
4 <requirement type="package" version="1.0.5">shigatyper</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 shigatyper -n "$input1.name" "$input1" "$input2" -vv > "$output1"
8 ]]></command>
9 <inputs>
10 <param type="data" name="input1" format="fastqsanger, fastqsanger.gz" />
11 <param type="data" name="input2" format="fastqsanger, fastqsanger.gz" />
12 </inputs>
13 <outputs>
14 <data name="output1" label="Shigella serotype prediction" format="tabular" />
15 </outputs>
16 <tests>
17 <test>
18 <param name="input1" value="CFSAN029786_S10_L001_R1_001.fastq.gz"/>
19 <param name="input2" value="CFSAN029786_S10_L001_R2_001.fastq.gz"/>
20 <output name="output1" file="output.tabular"/>
21 </test>
22 </tests>
23 <help><![CDATA[
24 usage: shigatyper [-h] [-n SAMPLE_NAME] [--verbose] [--version] read1 read2
25
26 positional arguments:
27 read1
28 read2
29
30
31 ]]></help>
32 <citations>
33 <citation type="bibtex">
34 @misc{githubshigatyper,
35 author = {LastTODO, FirstTODO},
36 year = {TODO},
37 title = {shigatyper},
38 publisher = {GitHub},
39 journal = {GitHub repository},
40 url = {https://github.com/CFSAN-Biostatistics/shigatyper},
41 }</citation>
42 </citations>
43 </tool>