--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cfsan_lexmapr2.xml	Wed Sep 14 10:39:29 2022 -0400
@@ -0,0 +1,129 @@
+<tool id="cfsan_lexmapr2" name="Lexmapr2" version="2.0+galaxy0">
+    <description>A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology Terms</description>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+        <requirement type="package">python-dateutil</requirement>
+        <requirement type="package">inflection</requirement>
+        <requirement type="package">matplotlib</requirement>
+        <requirement type="package">pandas</requirement>
+        <requirement type="package">nltk</requirement>
+        <requirement type="package">requests</requirement>
+        <requirement type="package">seaborn</requirement>
+        <requirement type="package">pygraphviz</requirement>
+    </requirements>
+    <version_command>python $__tool_directory__/lexmapr2.py --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    python $__tool_directory__/lexmapr2.py
+    #if ($embl_ont != ""):
+        -e $embl_ont
+    #end if
+    $no_ancestors
+    $bins
+    $full
+    $graph
+    #for $in_json in $input_json
+        #if $in_json
+            -u "$in_json"
+        #end if
+    #end for
+    ]]></command>
+    <environment_variables>
+        <environment_variable name="NLTK_DATA">/tool/tool-data/cfsan_lexmapr2/0/nltk_data</environment_variable>
+    </environment_variables>
+    <inputs>
+        <param name="input" type="data" format="csv" label="Input CSV"
+            help="First row should be a header and first column should be sample names" />
+        <param name="input_json" type="data" format="json" optional="true"
+            label="User defined bins in JSON format" />
+        <param name="embl_ont" type="text" optional="true" 
+            label="User defined comma-separated EMBL Ontology short names" />
+        <param name="bins" truevalue="-b" type="boolean" checked="true"
+            label="Classify samples into default bins" help="Default: true"/>
+        <param name="graph" truevalue="-g" type="boolean" checked="true"
+            label="Visualize summary of mapping and binning" help="Default: true"/>
+        <param name="full" truevalue="-f" type="boolean" checked="false"
+            label="Generate full output format" help="Default: false"/>
+        <param name="no_ancestors" truevalue="-a" type="boolean" checked="false"
+            label="Remove ancestral terms from output" help="Default: false"/>
+    </inputs>
+    <outputs>
+        <data name="lexmapr2_output" format="tsv" label="Lexmapr2: On ${on_string}" from_work_dir="lexmapr2_output.tsv"/>
+        <collection name="plots" type="list" label="Lexmapr2: Plots on ${on_string}">
+            <discover_datasets pattern=".*\.png" ext="png" directory="lexmapr_figures"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="input" value="test.csv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**Purpose**
+
+Lexmapr2 is a fork of Lexmapr (https://github.com/cidgoh/LexMapr) with the following added functionalitites:
+
+    ::
+
+        - pull ontology accession ids and definitions from EMBL-EBI via the API
+        - group mapped results by parent ontologies
+        - visualize mapping results
+
+----
+
+.. class:: infomark
+
+**Customization**
+
+By default, the FOODON and NCBITaxon ontologies are used. Users can define a comma-delimited list of ontology short names (https://www.ebi.ac.uk/ols/ontologies) flagged with '-e'. Bins are used to categorize matched ontologies by their parent ontologies. Users can override the default bins by flagging a JSON file with the '-u' option.
+
+Example JSON format to use a bin titled 'ncbi_taxon':
+
+    ::
+
+        {
+            "ncbi_taxon":{
+                "Actinopterygii":"NCBITaxon_7898",
+                "Ecdysozoa":"NCBITaxon_1206794",
+                "Echinodermata":"NCBITaxon_7586",
+                "Fungi":"NCBITaxon_4751",
+                "Mammalia":"NCBITaxon_40674",
+                "Sauropsida":"NCBITaxon_8457",
+                "Spiralia":"NCBITaxon_2697495",
+                "Viridiplantae":"NCBITaxon_33090"
+            }
+        }
+
+----
+
+.. class:: infomark
+
+**Outputs**
+
+The main output files are:
+
+    ::
+
+        - An tab-seperated file with possible matched annotations.
+        - A list of Lexmapr2 figures in PNG format.
+
+  ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @misc{github,
+            author = {Penn, Kayla},
+            year = {2022},
+            title = {LexMapr2},
+            publisher = {GitHub},
+            journal = {GitHub repository},
+            url = {https://github.com/CFSAN-Biostatistics/LexMapr2}}
+        </citation>
+        <citation type="bibtex">
+            @misc{GalaxyToolWrapper,
+            author = {Konganti, Kranti},
+            year = {2022}}
+        </citation>
+    </citations>
+</tool>