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annotate cfsan_lexmapr2.xml @ 0:91438d32ed58

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author kkonganti
date Wed, 14 Sep 2022 10:39:29 -0400
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children 6fc05c435932
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kkonganti@0 1 <tool id="cfsan_lexmapr2" name="Lexmapr2" version="2.0+galaxy0">
kkonganti@0 2 <description>A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology Terms</description>
kkonganti@0 3 <requirements>
kkonganti@0 4 <requirement type="package" version="3.7">python</requirement>
kkonganti@0 5 <requirement type="package">python-dateutil</requirement>
kkonganti@0 6 <requirement type="package">inflection</requirement>
kkonganti@0 7 <requirement type="package">matplotlib</requirement>
kkonganti@0 8 <requirement type="package">pandas</requirement>
kkonganti@0 9 <requirement type="package">nltk</requirement>
kkonganti@0 10 <requirement type="package">requests</requirement>
kkonganti@0 11 <requirement type="package">seaborn</requirement>
kkonganti@0 12 <requirement type="package">pygraphviz</requirement>
kkonganti@0 13 </requirements>
kkonganti@0 14 <version_command>python $__tool_directory__/lexmapr2.py --version</version_command>
kkonganti@0 15 <command detect_errors="exit_code"><![CDATA[
kkonganti@0 16 python $__tool_directory__/lexmapr2.py
kkonganti@0 17 #if ($embl_ont != ""):
kkonganti@0 18 -e $embl_ont
kkonganti@0 19 #end if
kkonganti@0 20 $no_ancestors
kkonganti@0 21 $bins
kkonganti@0 22 $full
kkonganti@0 23 $graph
kkonganti@0 24 #for $in_json in $input_json
kkonganti@0 25 #if $in_json
kkonganti@0 26 -u "$in_json"
kkonganti@0 27 #end if
kkonganti@0 28 #end for
kkonganti@0 29 ]]></command>
kkonganti@0 30 <environment_variables>
kkonganti@0 31 <environment_variable name="NLTK_DATA">/tool/tool-data/cfsan_lexmapr2/0/nltk_data</environment_variable>
kkonganti@0 32 </environment_variables>
kkonganti@0 33 <inputs>
kkonganti@0 34 <param name="input" type="data" format="csv" label="Input CSV"
kkonganti@0 35 help="First row should be a header and first column should be sample names" />
kkonganti@0 36 <param name="input_json" type="data" format="json" optional="true"
kkonganti@0 37 label="User defined bins in JSON format" />
kkonganti@0 38 <param name="embl_ont" type="text" optional="true"
kkonganti@0 39 label="User defined comma-separated EMBL Ontology short names" />
kkonganti@0 40 <param name="bins" truevalue="-b" type="boolean" checked="true"
kkonganti@0 41 label="Classify samples into default bins" help="Default: true"/>
kkonganti@0 42 <param name="graph" truevalue="-g" type="boolean" checked="true"
kkonganti@0 43 label="Visualize summary of mapping and binning" help="Default: true"/>
kkonganti@0 44 <param name="full" truevalue="-f" type="boolean" checked="false"
kkonganti@0 45 label="Generate full output format" help="Default: false"/>
kkonganti@0 46 <param name="no_ancestors" truevalue="-a" type="boolean" checked="false"
kkonganti@0 47 label="Remove ancestral terms from output" help="Default: false"/>
kkonganti@0 48 </inputs>
kkonganti@0 49 <outputs>
kkonganti@0 50 <data name="lexmapr2_output" format="tsv" label="Lexmapr2: On ${on_string}" from_work_dir="lexmapr2_output.tsv"/>
kkonganti@0 51 <collection name="plots" type="list" label="Lexmapr2: Plots on ${on_string}">
kkonganti@0 52 <discover_datasets pattern=".*\.png" ext="png" directory="lexmapr_figures"/>
kkonganti@0 53 </collection>
kkonganti@0 54 </outputs>
kkonganti@0 55 <tests>
kkonganti@0 56 <test expect_num_outputs="2">
kkonganti@0 57 <param name="input" value="test.csv"/>
kkonganti@0 58 </test>
kkonganti@0 59 </tests>
kkonganti@0 60 <help><![CDATA[
kkonganti@0 61
kkonganti@0 62 .. class:: infomark
kkonganti@0 63
kkonganti@0 64 **Purpose**
kkonganti@0 65
kkonganti@0 66 Lexmapr2 is a fork of Lexmapr (https://github.com/cidgoh/LexMapr) with the following added functionalitites:
kkonganti@0 67
kkonganti@0 68 ::
kkonganti@0 69
kkonganti@0 70 - pull ontology accession ids and definitions from EMBL-EBI via the API
kkonganti@0 71 - group mapped results by parent ontologies
kkonganti@0 72 - visualize mapping results
kkonganti@0 73
kkonganti@0 74 ----
kkonganti@0 75
kkonganti@0 76 .. class:: infomark
kkonganti@0 77
kkonganti@0 78 **Customization**
kkonganti@0 79
kkonganti@0 80 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 81
kkonganti@0 82 Example JSON format to use a bin titled 'ncbi_taxon':
kkonganti@0 83
kkonganti@0 84 ::
kkonganti@0 85
kkonganti@0 86 {
kkonganti@0 87 "ncbi_taxon":{
kkonganti@0 88 "Actinopterygii":"NCBITaxon_7898",
kkonganti@0 89 "Ecdysozoa":"NCBITaxon_1206794",
kkonganti@0 90 "Echinodermata":"NCBITaxon_7586",
kkonganti@0 91 "Fungi":"NCBITaxon_4751",
kkonganti@0 92 "Mammalia":"NCBITaxon_40674",
kkonganti@0 93 "Sauropsida":"NCBITaxon_8457",
kkonganti@0 94 "Spiralia":"NCBITaxon_2697495",
kkonganti@0 95 "Viridiplantae":"NCBITaxon_33090"
kkonganti@0 96 }
kkonganti@0 97 }
kkonganti@0 98
kkonganti@0 99 ----
kkonganti@0 100
kkonganti@0 101 .. class:: infomark
kkonganti@0 102
kkonganti@0 103 **Outputs**
kkonganti@0 104
kkonganti@0 105 The main output files are:
kkonganti@0 106
kkonganti@0 107 ::
kkonganti@0 108
kkonganti@0 109 - An tab-seperated file with possible matched annotations.
kkonganti@0 110 - A list of Lexmapr2 figures in PNG format.
kkonganti@0 111
kkonganti@0 112 ]]></help>
kkonganti@0 113 <citations>
kkonganti@0 114 <citation type="bibtex">
kkonganti@0 115 @misc{github,
kkonganti@0 116 author = {Penn, Kayla},
kkonganti@0 117 year = {2022},
kkonganti@0 118 title = {LexMapr2},
kkonganti@0 119 publisher = {GitHub},
kkonganti@0 120 journal = {GitHub repository},
kkonganti@0 121 url = {https://github.com/CFSAN-Biostatistics/LexMapr2}}
kkonganti@0 122 </citation>
kkonganti@0 123 <citation type="bibtex">
kkonganti@0 124 @misc{GalaxyToolWrapper,
kkonganti@0 125 author = {Konganti, Kranti},
kkonganti@0 126 year = {2022}}
kkonganti@0 127 </citation>
kkonganti@0 128 </citations>
kkonganti@0 129 </tool>