# HG changeset patch
# User iuc
# Date 1645475018 0
# Node ID b469f6d53d0692626aba5e2b0a06a97305c1e57f

"planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"

diff -r 000000000000 -r b469f6d53d06 legsta.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/legsta.xml	Mon Feb 21 20:23:38 2022 +0000
@@ -0,0 +1,66 @@
+<tool id="legsta" name="legsta" version="@TOOL_VERSION@" profile="20.01">
+    <description>Legionella pneumophila sequence based typing</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+
+    <command detect_errors="exit_code"><![CDATA[
+        legsta
+
+        $noheader
+        $csv
+
+        #for $i in $contigs
+            '$i'
+        #end for
+
+        > '$output'
+    ]]></command>
+
+    <inputs>
+        <param type="data" name="contigs" format="genbank,embl,gff,gff3,fasta,fasta.gz,fastq,fastq.gz,clustal,stockholm" multiple="true" label="Contigs" help="One or more input files in FASTA, FASTQ, Genbank, EMBL, Clustal, Stockholm or GFF format." />
+        <param name="noheader" type="boolean" argument="--noheader" truevalue="--noheader" falsevalue="" label="Remove table header" help="Removes the table header from the output (ie. FILE SBT flaA ...)" />
+        <param name="csv" type="boolean" argument="--csv" truevalue="--csv" falsevalue="" label="CSV output" help="Prints the output in comma-separated value format instead of tab-separated value format." />
+    </inputs>
+
+    <outputs>
+        <data name="output" format="tabular">
+            <change_format>
+                <when input="csv" value="--csv" format="csv" />
+                <when input="csv" value="" format="tabular" />
+            </change_format>
+        </data>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="contigs" ftype="fasta" value="NC_006368.fna.bz2"/>
+            <param name="csv" value="true"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="SBT,flaA,pilE,asd,mip,mompS,proA,neuA" />
+                    <has_text text="1,1,4,3,1,1,1,1" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+
+    <help>
+In silico sequence based typing (SBT) of Legionella pneumophila.
+
+The purpose of the Legionella pneumophila SBT scheme is to provide a rapid and easily comparable method for the epidemiological typing of clinical and environmental isolates of Legionella pneumophila in outbreak investigations.
+    </help>
+
+    <citations>
+        <citation type="bibtex">
+@misc{githublegsta,
+  author = {Seemann, Torsten and Da Silva, Anders Goncalves, and Buultjens, Andrew, and Kwong, Jason},
+  title = {legsta},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/tseemann/legsta},
+}</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r b469f6d53d06 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Feb 21 20:23:38 2022 +0000
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">legsta</requirement>
+        </requirements>
+    </xml>
+    <token name="@TOOL_VERSION@">0.5.1</token>
+</macros>
diff -r 000000000000 -r b469f6d53d06 test-data/NC_006368.fna.bz2
Binary file test-data/NC_006368.fna.bz2 has changed