--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abritamr.xml	Tue May 09 11:09:18 2023 +0000
@@ -0,0 +1,95 @@
+<tool id="abritamr" name="abriTAMR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>AMR gene detection with AMRFinderPlus</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.14</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">22.05</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">abritamr</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+abritamr run
+    --contigs '$input_tsv'
+#if $species:
+    --species '$species'
+#end if
+#if $identity:
+    --identity '$identity'
+#end if
+    --jobs \${GALAXY_SLOTS:-4}
+]]></command>
+    <configfiles>
+        <configfile name="input_tsv">
+#for $i in $contig:
+${i.element_identifier}	${i}
+#end for
+        </configfile>
+    </configfiles>
+    <inputs>
+        <param name="contig" type="data" format="fasta" multiple="true" label="Input contigs"/>
+        <param argument="species" type="select" multiple="false" optional="true" label="Specify species to aquire resistance mechanisms as point mutations">
+            <option value="Neisseria">Neisseria</option>
+            <option value="Clostridioides_difficile">Clostridioides difficile</option>
+            <option value="Acinetobacter_baumannii">Acinetobacter baumannii</option>
+            <option value="Campylobacter">Campylobacter</option>
+            <option value="Enterococcus_faecalis">Enterococcus faecalis</option>
+            <option value="Enterococcus_faecium">Enterococcus faecium</option>
+            <option value="Escherichia">Escherichia</option>
+            <option value="Klebsiella">Klebsiella</option>
+            <option value="Salmonella">Salmonella</option>
+            <option value="Staphylococcus_aureus">Staphylococcus aureus</option>
+            <option value="Staphylococcus_pseudintermedius">Staphylococcus pseudintermedius</option>
+            <option value="Streptococcus_agalactiae">Streptococcus agalactiae</option>
+            <option value="Streptococcus_pneumoniae">Streptococcus pneumoniae</option>
+            <option value="Streptococcus_pyogenes">Streptococcus pyogenes</option>
+        </param>
+        <param argument="identity" value="0.9" type="float" optional="true" min="0.0" max="1" label="Minimum identity of matches with armfinder. Default: 0.9, unless curated threshold is present for the gene."/>
+        <param name="log_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate log file."/>
+    </inputs>
+    <outputs>
+        <data name="abriTAMR_output" format="txt" label="${tool.name} on ${on_string}: abriTAMR.txt" from_work_dir="abritamr.txt" />
+        <data name="matches_summary" format="txt" label="${tool.name} on ${on_string}: matches summary" from_work_dir="summary_matches.txt"/>
+        <data name="partials_summary" format="txt" label="${tool.name} on ${on_string}: partials summary" from_work_dir="summary_partials.txt"/>
+        <data name="virulence_summary" format="txt" label="${tool.name} on ${on_string}: virulence summary" from_work_dir="summary_virulence.txt"/>
+        <data name="log" format="txt" label="${tool.name} on ${on_string}: log file" from_work_dir="abritamr.log">
+            <filter>log_file</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- Single sample, with logfile -->
+        <test expect_num_outputs="5">
+            <param name="contig" value="CP009102.1.fasta" />
+            <param name="log_file" value="true" />
+            <output name="virulence_summary" ftype="txt">
+                <assert_contents>
+                    <has_n_lines n="2"/>
+                    <has_text text="iroB,iroC,sinH"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Multiple samples, no logfile -->
+        <test expect_num_outputs="4">
+            <param name="contig" value="NC_003198.1_1kb.fasta,NC_011750.1_1kb.fasta" />
+            <param name="species" value="Salmonella" />
+            <param name="identity" value="0.9" />
+            <param name="log_file" value="false" />
+            <output name="virulence_summary" ftype="txt">
+                <assert_contents>
+                    <has_n_lines n="3"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+*Taming the AMR beast*
+
+abriTAMR is an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. abriTAMR is accredited by NATA for use in reporting the presence of reportable AMR genes in Victoria Australia.
+    + Acquired resistance mechanims in the form of point mutations (restricted to subset of species)
+    + Streamlined output.
+    + Presence of virulence factors
+    </help>
+    <citations>
+        <citation type="doi">10.5281/zenodo.7370627</citation>
+    </citations>
+</tool>