kkonganti@0: <tool id="cfsan_lexmapr2" name="Lexmapr2" version="2.0+galaxy0">
kkonganti@0:     <description>A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology Terms</description>
kkonganti@0:     <requirements>
kkonganti@0:         <requirement type="package" version="3.7">python</requirement>
kkonganti@0:         <requirement type="package">python-dateutil</requirement>
kkonganti@0:         <requirement type="package">inflection</requirement>
kkonganti@0:         <requirement type="package">matplotlib</requirement>
kkonganti@0:         <requirement type="package">pandas</requirement>
kkonganti@0:         <requirement type="package">nltk</requirement>
kkonganti@0:         <requirement type="package">requests</requirement>
kkonganti@0:         <requirement type="package">seaborn</requirement>
kkonganti@0:         <requirement type="package">pygraphviz</requirement>
kkonganti@0:     </requirements>
kkonganti@0:     <version_command>python $__tool_directory__/lexmapr2.py --version</version_command>
kkonganti@0:     <command detect_errors="exit_code"><![CDATA[
kkonganti@12:     echo \$PYTHONPATH 1>&2;
kkonganti@4:     mkdir -p lexmapr2-input || exit 1;
kkonganti@4:     ln -sf '$input' './lexmapr2-input/$input.name';
kkonganti@0:     python $__tool_directory__/lexmapr2.py
kkonganti@0:     #if ($embl_ont != ""):
kkonganti@0:         -e $embl_ont
kkonganti@0:     #end if
kkonganti@3:     #if (str($no_ancestors) != "false"):
kkonganti@3:         $no_ancestors
kkonganti@3:     #end if
kkonganti@3:     #if (str($bins) != "false"):
kkonganti@3:         $bins
kkonganti@3:     #end if
kkonganti@3:     #if (str($full) != "false"):
kkonganti@3:         $full
kkonganti@3:     #end if
kkonganti@3:     #if (str($graph) != "false"):
kkonganti@3:         $graph
kkonganti@3:     #end if
kkonganti@3:     #if $input_json.json_is_set:
kkonganti@1:         -u "$input_json.upload"
kkonganti@1:     #end if
kkonganti@4:     ./lexmapr2-input/$input.name
kkonganti@0:     ]]></command>
kkonganti@0:     <environment_variables>
kkonganti@0:         <environment_variable name="NLTK_DATA">/tool/tool-data/cfsan_lexmapr2/0/nltk_data</environment_variable>
kkonganti@11:         <environment_variable name="PYTHONPATH">/tool/tool-data/cfsan_lexmapr2/0</environment_variable>
kkonganti@0:     </environment_variables>
kkonganti@0:     <inputs>
kkonganti@0:         <param name="input" type="data" format="csv" label="Input CSV"
kkonganti@0:             help="First row should be a header and first column should be sample names" />
kkonganti@2:         <param name="embl_ont" type="text" optional="true" 
kkonganti@2:             label="User defined comma-separated EMBL Ontology short names" />
kkonganti@1:         <conditional name="input_json">
kkonganti@1:             <param name="json_is_set" type="boolean" label="Use User defined bins in JSON format?" />
kkonganti@1:             <when value="true">
kkonganti@1:                 <param name="upload" type="data" format="json" label="User defined bins" />
kkonganti@1:             </when>
kkonganti@1:             <when value="false">
kkonganti@1:             </when>
kkonganti@1:         </conditional>
kkonganti@0:         <param name="bins" truevalue="-b" type="boolean" checked="true"
kkonganti@0:             label="Classify samples into default bins" help="Default: true"/>
kkonganti@0:         <param name="graph" truevalue="-g" type="boolean" checked="true"
kkonganti@0:             label="Visualize summary of mapping and binning" help="Default: true"/>
kkonganti@0:         <param name="full" truevalue="-f" type="boolean" checked="false"
kkonganti@0:             label="Generate full output format" help="Default: false"/>
kkonganti@0:         <param name="no_ancestors" truevalue="-a" type="boolean" checked="false"
kkonganti@0:             label="Remove ancestral terms from output" help="Default: false"/>
kkonganti@0:     </inputs>
kkonganti@0:     <outputs>
kkonganti@0:         <data name="lexmapr2_output" format="tsv" label="Lexmapr2: On ${on_string}" from_work_dir="lexmapr2_output.tsv"/>
kkonganti@0:         <collection name="plots" type="list" label="Lexmapr2: Plots on ${on_string}">
kkonganti@0:             <discover_datasets pattern=".*\.png" ext="png" directory="lexmapr_figures"/>
kkonganti@0:         </collection>
kkonganti@0:     </outputs>
kkonganti@0:     <tests>
kkonganti@0:         <test expect_num_outputs="2">
kkonganti@0:             <param name="input" value="test.csv"/>
kkonganti@0:         </test>
kkonganti@0:     </tests>
kkonganti@0:     <help><![CDATA[
kkonganti@0: 
kkonganti@0: .. class:: infomark
kkonganti@0: 
kkonganti@0: **Purpose**
kkonganti@0: 
kkonganti@0: Lexmapr2 is a fork of Lexmapr (https://github.com/cidgoh/LexMapr) with the following added functionalitites:
kkonganti@0: 
kkonganti@0:     ::
kkonganti@0: 
kkonganti@0:         - pull ontology accession ids and definitions from EMBL-EBI via the API
kkonganti@0:         - group mapped results by parent ontologies
kkonganti@0:         - visualize mapping results
kkonganti@0: 
kkonganti@0: ----
kkonganti@0: 
kkonganti@0: .. class:: infomark
kkonganti@0: 
kkonganti@0: **Customization**
kkonganti@0: 
kkonganti@0: 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.
kkonganti@0: 
kkonganti@0: Example JSON format to use a bin titled 'ncbi_taxon':
kkonganti@0: 
kkonganti@0:     ::
kkonganti@0: 
kkonganti@0:         {
kkonganti@0:             "ncbi_taxon":{
kkonganti@0:                 "Actinopterygii":"NCBITaxon_7898",
kkonganti@0:                 "Ecdysozoa":"NCBITaxon_1206794",
kkonganti@0:                 "Echinodermata":"NCBITaxon_7586",
kkonganti@0:                 "Fungi":"NCBITaxon_4751",
kkonganti@0:                 "Mammalia":"NCBITaxon_40674",
kkonganti@0:                 "Sauropsida":"NCBITaxon_8457",
kkonganti@0:                 "Spiralia":"NCBITaxon_2697495",
kkonganti@0:                 "Viridiplantae":"NCBITaxon_33090"
kkonganti@0:             }
kkonganti@0:         }
kkonganti@0: 
kkonganti@0: ----
kkonganti@0: 
kkonganti@0: .. class:: infomark
kkonganti@0: 
kkonganti@0: **Outputs**
kkonganti@0: 
kkonganti@0: The main output files are:
kkonganti@0: 
kkonganti@0:     ::
kkonganti@0: 
kkonganti@0:         - An tab-seperated file with possible matched annotations.
kkonganti@0:         - A list of Lexmapr2 figures in PNG format.
kkonganti@0: 
kkonganti@0:   ]]></help>
kkonganti@0:     <citations>
kkonganti@0:         <citation type="bibtex">
kkonganti@0:             @misc{github,
kkonganti@0:             author = {Penn, Kayla},
kkonganti@0:             year = {2022},
kkonganti@0:             title = {LexMapr2},
kkonganti@0:             publisher = {GitHub},
kkonganti@0:             journal = {GitHub repository},
kkonganti@0:             url = {https://github.com/CFSAN-Biostatistics/LexMapr2}}
kkonganti@0:         </citation>
kkonganti@0:         <citation type="bibtex">
kkonganti@0:             @misc{GalaxyToolWrapper,
kkonganti@0:             author = {Konganti, Kranti},
kkonganti@2:             year = {2022},
kkonganti@2:             title = {Lexmapr2 Tool Wrapper for Galaxy},
kkonganti@2:             journal = {GalaxyTrakr Tool repository},
kkonganti@2:             url = {https://toolrepo.galaxytrakr.org/repository/browse_repository?id=e00d4fc8bba8b6c5}}
kkonganti@0:         </citation>
kkonganti@0:     </citations>
kkonganti@0: </tool>