Mercurial > repos > jpayne > shigatyper
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| author | jpayne |
|---|---|
| date | Thu, 27 Jun 2019 13:46:42 -0400 |
| parents | |
| children | ce999a6ef3ba |
| rev | line source |
|---|---|
| jpayne@0 | 1 <tool id="shigatyper" name="ShigaTyper" version="1.0.5"> |
| jpayne@0 | 2 <description>Shigella genoserotyping</description> |
| jpayne@0 | 3 <requirements> |
| jpayne@0 | 4 <requirement type="package" version="1.0.5">shigatyper</requirement> |
| jpayne@0 | 5 </requirements> |
| jpayne@0 | 6 <command detect_errors="exit_code"><![CDATA[ |
| jpayne@0 | 7 shigatyper -n "$input1.name" "$input1" "$input2" -vv > "$output1" |
| jpayne@0 | 8 ]]></command> |
| jpayne@0 | 9 <inputs> |
| jpayne@0 | 10 <param type="data" name="input1" format="fastqsanger, fastqsanger.gz" /> |
| jpayne@0 | 11 <param type="data" name="input2" format="fastqsanger, fastqsanger.gz" /> |
| jpayne@0 | 12 </inputs> |
| jpayne@0 | 13 <outputs> |
| jpayne@0 | 14 <data name="output1" label="Shigella serotype prediction" format="tabular" /> |
| jpayne@0 | 15 </outputs> |
| jpayne@0 | 16 <tests> |
| jpayne@0 | 17 <test> |
| jpayne@0 | 18 <param name="input1" value="CFSAN029786_S10_L001_R1_001.fastq.gz"/> |
| jpayne@0 | 19 <param name="input2" value="CFSAN029786_S10_L001_R2_001.fastq.gz"/> |
| jpayne@0 | 20 <output name="output1" file="output.tabular"/> |
| jpayne@0 | 21 </test> |
| jpayne@0 | 22 </tests> |
| jpayne@0 | 23 <help><![CDATA[ |
| jpayne@0 | 24 usage: shigatyper [-h] [-n SAMPLE_NAME] [--verbose] [--version] read1 read2 |
| jpayne@0 | 25 |
| jpayne@0 | 26 positional arguments: |
| jpayne@0 | 27 read1 |
| jpayne@0 | 28 read2 |
| jpayne@0 | 29 |
| jpayne@0 | 30 |
| jpayne@0 | 31 ]]></help> |
| jpayne@0 | 32 <citations> |
| jpayne@0 | 33 <citation type="bibtex"> |
| jpayne@0 | 34 @misc{githubshigatyper, |
| jpayne@0 | 35 author = {LastTODO, FirstTODO}, |
| jpayne@0 | 36 year = {TODO}, |
| jpayne@0 | 37 title = {shigatyper}, |
| jpayne@0 | 38 publisher = {GitHub}, |
| jpayne@0 | 39 journal = {GitHub repository}, |
| jpayne@0 | 40 url = {https://github.com/CFSAN-Biostatistics/shigatyper}, |
| jpayne@0 | 41 }</citation> |
| jpayne@0 | 42 </citations> |
| jpayne@0 | 43 </tool> |