Mercurial > repos > jpayne > shigatyper
changeset 0:00c8dbe0549a
planemo upload
| author | jpayne |
|---|---|
| date | Thu, 27 Jun 2019 13:46:42 -0400 |
| parents | |
| children | 4b327e1f39f3 |
| files | shigatyper.xml test-data/CFSAN029786_S10_L001_R1_001.fastq.gz test-data/CFSAN029786_S10_L001_R2_001.fastq.gz test-data/output.tabular |
| diffstat | 4 files changed, 45 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/shigatyper.xml Thu Jun 27 13:46:42 2019 -0400 @@ -0,0 +1,43 @@ +<tool id="shigatyper" name="ShigaTyper" version="1.0.5"> + <description>Shigella genoserotyping</description> + <requirements> + <requirement type="package" version="1.0.5">shigatyper</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + shigatyper -n "$input1.name" "$input1" "$input2" -vv > "$output1" + ]]></command> + <inputs> + <param type="data" name="input1" format="fastqsanger, fastqsanger.gz" /> + <param type="data" name="input2" format="fastqsanger, fastqsanger.gz" /> + </inputs> + <outputs> + <data name="output1" label="Shigella serotype prediction" format="tabular" /> + </outputs> + <tests> + <test> + <param name="input1" value="CFSAN029786_S10_L001_R1_001.fastq.gz"/> + <param name="input2" value="CFSAN029786_S10_L001_R2_001.fastq.gz"/> + <output name="output1" file="output.tabular"/> + </test> + </tests> + <help><![CDATA[ +usage: shigatyper [-h] [-n SAMPLE_NAME] [--verbose] [--version] read1 read2 + +positional arguments: + read1 + read2 + + + ]]></help> + <citations> + <citation type="bibtex"> +@misc{githubshigatyper, + author = {LastTODO, FirstTODO}, + year = {TODO}, + title = {shigatyper}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/CFSAN-Biostatistics/shigatyper}, +}</citation> + </citations> +</tool> \ No newline at end of file