--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IslandPath.xml	Fri Jan 24 18:01:06 2020 -0500
@@ -0,0 +1,54 @@
+<tool id="islandpath" name="IslandPath" version="1.0.4" profile="16.04">
+    <description>predict genomic islands in bacterial and archaeal genomes based on the presence of dinucleotide biases and mobility genes</description>
+    <edam_topics>
+        <edam_topic>topic_0194</edam_topic>
+        <edam_topic>topic_0091</edam_topic>
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_0362</edam_operation>
+    </edam_operations>
+    <requirements>
+        <requirement type="package" version="1.0.4">islandpath</requirement>
+    </requirements>
+    <version_command><![CDATA[ echo "1.0.4" ]]></version_command>
+    <command detect_errors="aggressive"><![CDATA[
+    #import os
+    #if $input.is_of_type("embl")
+        #set inp=$os.path.basename(str($input))+".embl"
+    #else
+        #set inp=$os.path.basename(str($input))+".gbk"
+    #end if
+    ln -s "$input" "$inp"
+    && islandpath "$inp" "$output"
+    ]]></command>
+    <inputs>
+        <param type="data" format="genbank,embl" name="input" argument="input" label="Input" optional="false"/>
+    </inputs>
+    <outputs>
+        <data format="gff" name="output" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="test-data/test.embl" ftype="embl" />
+            <output name="output" checksum="sha256:36d25184326c3415001675921bf76be588edce9fe3313b8082c3eeac83dcf958" ftype="gff" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        [IslandPath](http://www.pathogenomics.sfu.ca/islandpath/) was originally designed to aid to the identification of prokaryotic genomics islands (GIs),
+        including pathogenicity islands, of potentially horizontally transferred genes by visualizing several common characteristics of GIs such as abnormal
+        sequence composition or the presence of genes that functionally related to mobile elements (termed mobility genes).
+        
+        Further studies (see [Hsiao et al 2005](http://www.ncbi.nlm.nih.gov/pubmed/16299586)) used dinucleotide sequence compostion bias and the presence of
+        mobility genes to develop a dataset of GIs (IslandPath DIMOB) for multiple organisms and revealed that these genomic regions contain higher
+        proportions of novel genes.
+        
+        A recent study (see Langille et al 2008 (submitted)), developed a new method called [IslandPick](http://www.pathogenomics.sfu.ca/islandpick/)
+        that used comparative genomics to develop stringent data sets of GIs and non-GIs. These positive and negative data sets that were not based on
+        sequence composition bias allowed for an independent review of several previously published GI predictors. Although the overall accuracy of
+        several of the tools were similar, IslandPath DIMOB was shown to have the highest accuracy.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.5281/zenodo.3364789</citation>
+        <citation type="doi">10.1093/bioinformatics/bty095</citation>
+    </citations>
+</tool>