Mercurial > repos > estrain > emmtyper
changeset 1:599371de692d draft
Uploaded
| author | estrain |
|---|---|
| date | Fri, 31 Mar 2023 17:15:39 +0000 |
| parents | e72652c6edb9 |
| children | 0817dc5dc7f7 |
| files | emmtyper.xml emmtyper/emmtyper.xml |
| diffstat | 2 files changed, 76 insertions(+), 76 deletions(-) [+] |
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--- a/emmtyper.xml Fri Mar 31 17:14:38 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ -l<tool id="emmtyper" name="emm-typing of S. pyogenes" version="0.1.0+galaxy0"> - <requirements> - <requirement type="package">emmtyper</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - emmtyper -o '$output1' '$input1' - ]]></command> - <inputs> - <param type="data" name="input1" format="fasta" /> - </inputs> - <outputs> - <data name="output1" format="txt" from_work_dir="results.txt" /> - </outputs> - <help><![CDATA[ - Usage: emmtyper [OPTIONS] [FASTA]... - - Welcome to emmtyper. - - Usage: - - emmtyper *.fasta - -Options: - --version Show the version and exit. - -w, --workflow [blast|pcr] Choose workflow [default: blast] - -d, --blast_db TEXT Path to EMM BLAST DB - -k, --keep Keep BLAST and isPcr output files. - -d, --cluster-distance INTEGER Distance between cluster of matches to - consider as different clusters. [default: - 500] - -o, --output TEXT Output stream. Path to file for output to a - file. [default: stdout] - -f, --output-format [short|verbose|visual] - Output format. - --dust [yes|no|level window linker] - [BLAST] Filter query sequence with DUST. - [default: no] - --percent-identity INTEGER [BLAST] Minimal percent identity of - sequence. [default: 95] - --culling-limit INTEGER [BLAST] Total hits to return in a position. - [default: 5] - --mismatch INTEGER [BLAST] Threshold for number of mismatch to - allow in BLAST hit. [default: 4] - --align-diff INTEGER [BLAST] Threshold for difference between - alignment length and subject length in BLAST - hit. [default: 5] - --gap INTEGER [BLAST] Threshold gap to allow in BLAST hit. - [default: 2] - --blast-path TEXT [BLAST] Specify full path to blastn - executable. - --primer-db TEXT [isPcr] PCR primer. Text file with 3 - columns: Name, Forward Primer, Reverse - Primer. - --min-perfect INTEGER [isPcr] Minimum size of perfect match at 3' - primer end. [default: 15] - --min-good INTEGER [isPcr] Minimum size where there must be 2 - matches for each mismatch. [default: 15] - --max-size INTEGER [isPcr] Maximum size of PCR product. - [default: 2000] - --ispcr-path TEXT [isPcr] Specify full path to isPcr - executable. - --help Show this message and exit. - - ]]></help> - <citations> - <citation type="bibtex"> -@misc{githubemmtyper, - author = {LastTODO, FirstTODO}, - year = {TODO}, - title = {emmtyper}, - publisher = {GitHub}, - journal = {GitHub repository}, - url = {https://github.com/MDU-PHL/emmtyper}, -}</citation> - </citations> -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/emmtyper/emmtyper.xml Fri Mar 31 17:15:39 2023 +0000 @@ -0,0 +1,76 @@ +l<tool id="emmtyper" name="emm-typing of S. pyogenes" version="0.1.0+galaxy0"> + <requirements> + <requirement type="package">emmtyper</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + emmtyper -o '$output1' '$input1' + ]]></command> + <inputs> + <param type="data" name="input1" format="fasta" /> + </inputs> + <outputs> + <data name="output1" format="txt" from_work_dir="results.txt" /> + </outputs> + <help><![CDATA[ + Usage: emmtyper [OPTIONS] [FASTA]... + + Welcome to emmtyper. + + Usage: + + emmtyper *.fasta + +Options: + --version Show the version and exit. + -w, --workflow [blast|pcr] Choose workflow [default: blast] + -d, --blast_db TEXT Path to EMM BLAST DB + -k, --keep Keep BLAST and isPcr output files. + -d, --cluster-distance INTEGER Distance between cluster of matches to + consider as different clusters. [default: + 500] + -o, --output TEXT Output stream. Path to file for output to a + file. [default: stdout] + -f, --output-format [short|verbose|visual] + Output format. + --dust [yes|no|level window linker] + [BLAST] Filter query sequence with DUST. + [default: no] + --percent-identity INTEGER [BLAST] Minimal percent identity of + sequence. [default: 95] + --culling-limit INTEGER [BLAST] Total hits to return in a position. + [default: 5] + --mismatch INTEGER [BLAST] Threshold for number of mismatch to + allow in BLAST hit. [default: 4] + --align-diff INTEGER [BLAST] Threshold for difference between + alignment length and subject length in BLAST + hit. [default: 5] + --gap INTEGER [BLAST] Threshold gap to allow in BLAST hit. + [default: 2] + --blast-path TEXT [BLAST] Specify full path to blastn + executable. + --primer-db TEXT [isPcr] PCR primer. Text file with 3 + columns: Name, Forward Primer, Reverse + Primer. + --min-perfect INTEGER [isPcr] Minimum size of perfect match at 3' + primer end. [default: 15] + --min-good INTEGER [isPcr] Minimum size where there must be 2 + matches for each mismatch. [default: 15] + --max-size INTEGER [isPcr] Maximum size of PCR product. + [default: 2000] + --ispcr-path TEXT [isPcr] Specify full path to isPcr + executable. + --help Show this message and exit. + + ]]></help> + <citations> + <citation type="bibtex"> +@misc{githubemmtyper, + author = {LastTODO, FirstTODO}, + year = {TODO}, + title = {emmtyper}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/MDU-PHL/emmtyper}, +}</citation> + </citations> +</tool>