Mercurial > repos > nml > sistr_cmd
changeset 5:24a7a95867b0 draft default tip
"planemo upload commit 683b11f79a83cf9e1563e46a75919157fa1136d4"
| author | nml |
|---|---|
| date | Fri, 19 Mar 2021 20:09:37 +0000 |
| parents | 17fcac7ddf54 |
| children | |
| files | README.md sistr_cmd.xml |
| diffstat | 2 files changed, 15 insertions(+), 3 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri Mar 19 20:09:37 2021 +0000 @@ -0,0 +1,12 @@ +# SISTR - Salmonella In Silico Typing Resource (SISTR) commandline tool + +`SISTR` is a standalone serotyping module for *Salmonella* typing. The tool supports assembled genomes. + +This Galaxy wrapper makes this tool accessible via Galaxy Project server and allows integration into workflows. Galaxy workflows include assembly and reporting steps for large sample sizes and are available to be installed from the main repository at <https://github.com/phac-nml/sistr_cmd> + +The tool can also be accessed via public instance at Galaxy EU at <https://usegalaxy.eu/root?tool_id=sistr_cmd> + +# Citation +If you find this tool useful, please cite as + +><cite> The *Salmonella In Silico* Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft *Salmonella* genome assemblies. Catherine Yoshida, Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor P.J. Gannon, John H.E. Nash, Eduardo N. Taboada. PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101 </cite>
--- a/sistr_cmd.xml Thu Aug 06 11:48:49 2020 -0400 +++ b/sistr_cmd.xml Fri Mar 19 20:09:37 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="sistr_cmd" name="sistr_cmd" version="@VERSION@"> +<tool id="sistr_cmd" name="sistr_cmd" version="@VERSION@+galaxy1"> <description> Salmonella In Silico Typing Resource commandline tool for serovar prediction </description> @@ -14,7 +14,7 @@ <command><![CDATA[ sistr #for $fasta in $input_fastas - -i '$fasta' '${$fasta.name.replace("." + $fasta.ext, "")}' + -i '$fasta' '${$fasta.element_identifier.replace("." + $fasta.ext, "")}' #end for -f $output_format -o sistr-report.$output_format @@ -39,7 +39,7 @@ optional="false" multiple="true" format="fasta" - /> + /> <param name="output_format" type="select"