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annotate cfsan_lexmapr2.xml @ 21:a86bcf3ea8a6

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"planemo upload"
author kkonganti
date Wed, 09 Nov 2022 09:08:00 -0500
parents 0be9a7117ba5
children 880f156d0454
rev   line source
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 $__tool_directory__/lexmapr2.py --version</version_command>
kkonganti@0 15 <command detect_errors="exit_code"><![CDATA[
kkonganti@4 16 mkdir -p lexmapr2-input || exit 1;
kkonganti@13 17 ln -sf '/tool/tool-data/cfsan_lexmapr2/0/lexmapr' .;
kkonganti@4 18 ln -sf '$input' './lexmapr2-input/$input.name';
kkonganti@0 19 python $__tool_directory__/lexmapr2.py
kkonganti@0 20 #if ($embl_ont != ""):
kkonganti@0 21 -e $embl_ont
kkonganti@0 22 #end if
kkonganti@3 23 #if (str($no_ancestors) != "false"):
kkonganti@3 24 $no_ancestors
kkonganti@3 25 #end if
kkonganti@3 26 #if (str($bins) != "false"):
kkonganti@3 27 $bins
kkonganti@3 28 #end if
kkonganti@3 29 #if (str($full) != "false"):
kkonganti@3 30 $full
kkonganti@3 31 #end if
kkonganti@3 32 #if (str($graph) != "false"):
kkonganti@3 33 $graph
kkonganti@3 34 #end if
kkonganti@3 35 #if $input_json.json_is_set:
kkonganti@1 36 -u "$input_json.upload"
kkonganti@1 37 #end if
kkonganti@21 38 -p 20
kkonganti@15 39 -o lexmapr2_output.tsv
kkonganti@17 40 ./lexmapr2-input/$input.name;
kkonganti@17 41 mv 'lexmapr_run.log' 'lexmapr2_run_log.txt' || exit 1;
kkonganti@0 42 ]]></command>
kkonganti@0 43 <environment_variables>
kkonganti@0 44 <environment_variable name="NLTK_DATA">/tool/tool-data/cfsan_lexmapr2/0/nltk_data</environment_variable>
kkonganti@14 45 <environment_variable name="PYTHONPATH">/tool/tool-data/cfsan_lexmapr2/0</environment_variable>
kkonganti@0 46 </environment_variables>
kkonganti@0 47 <inputs>
kkonganti@0 48 <param name="input" type="data" format="csv" label="Input CSV"
kkonganti@0 49 help="First row should be a header and first column should be sample names" />
kkonganti@2 50 <param name="embl_ont" type="text" optional="true"
kkonganti@2 51 label="User defined comma-separated EMBL Ontology short names" />
kkonganti@1 52 <conditional name="input_json">
kkonganti@1 53 <param name="json_is_set" type="boolean" label="Use User defined bins in JSON format?" />
kkonganti@1 54 <when value="true">
kkonganti@1 55 <param name="upload" type="data" format="json" label="User defined bins" />
kkonganti@1 56 </when>
kkonganti@1 57 <when value="false">
kkonganti@1 58 </when>
kkonganti@1 59 </conditional>
kkonganti@20 60 <param name="bins" truevalue="-b" type="boolean" checked="false"
kkonganti@20 61 label="Classify samples into default bins" help="Default: false. Turning on this option may increase run time."/>
kkonganti@20 62 <param name="graph" truevalue="-g" type="boolean" checked="false"
kkonganti@20 63 label="Visualize summary of mapping and binning" help="Default: false. Turning on this option may increase run time."/>
kkonganti@15 64 <param name="full" truevalue="-f" type="boolean" checked="true"
kkonganti@15 65 label="Generate full output format" help="Default: true"/>
kkonganti@0 66 <param name="no_ancestors" truevalue="-a" type="boolean" checked="false"
kkonganti@0 67 label="Remove ancestral terms from output" help="Default: false"/>
kkonganti@0 68 </inputs>
kkonganti@0 69 <outputs>
kkonganti@16 70 <data name="lexmapr2_output" format="tsv" label="Lexmapr2: Results On ${on_string}" from_work_dir="lexmapr2_output.tsv"/>
kkonganti@0 71 <collection name="plots" type="list" label="Lexmapr2: Plots on ${on_string}">
kkonganti@19 72 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" format="png" directory="lexmapr_figures"/>
kkonganti@0 73 </collection>
kkonganti@17 74 <data name="lexmapr2_log" format="txt" label="Lexmapr2: Log On ${on_string}" from_work_dir="lexmapr2_run_log.txt"/>
kkonganti@0 75 </outputs>
kkonganti@0 76 <tests>
kkonganti@0 77 <test expect_num_outputs="2">
kkonganti@0 78 <param name="input" value="test.csv"/>
kkonganti@0 79 </test>
kkonganti@0 80 </tests>
kkonganti@0 81 <help><![CDATA[
kkonganti@0 82
kkonganti@0 83 .. class:: infomark
kkonganti@0 84
kkonganti@0 85 **Purpose**
kkonganti@0 86
kkonganti@0 87 Lexmapr2 is a fork of Lexmapr (https://github.com/cidgoh/LexMapr) with the following added functionalitites:
kkonganti@0 88
kkonganti@0 89 ::
kkonganti@0 90
kkonganti@0 91 - pull ontology accession ids and definitions from EMBL-EBI via the API
kkonganti@0 92 - group mapped results by parent ontologies
kkonganti@0 93 - visualize mapping results
kkonganti@0 94
kkonganti@0 95 ----
kkonganti@0 96
kkonganti@0 97 .. class:: infomark
kkonganti@0 98
kkonganti@0 99 **Customization**
kkonganti@0 100
kkonganti@0 101 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@0 102
kkonganti@0 103 Example JSON format to use a bin titled 'ncbi_taxon':
kkonganti@0 104
kkonganti@0 105 ::
kkonganti@0 106
kkonganti@0 107 {
kkonganti@0 108 "ncbi_taxon":{
kkonganti@0 109 "Actinopterygii":"NCBITaxon_7898",
kkonganti@0 110 "Ecdysozoa":"NCBITaxon_1206794",
kkonganti@0 111 "Echinodermata":"NCBITaxon_7586",
kkonganti@0 112 "Fungi":"NCBITaxon_4751",
kkonganti@0 113 "Mammalia":"NCBITaxon_40674",
kkonganti@0 114 "Sauropsida":"NCBITaxon_8457",
kkonganti@0 115 "Spiralia":"NCBITaxon_2697495",
kkonganti@0 116 "Viridiplantae":"NCBITaxon_33090"
kkonganti@0 117 }
kkonganti@0 118 }
kkonganti@0 119
kkonganti@0 120 ----
kkonganti@0 121
kkonganti@0 122 .. class:: infomark
kkonganti@0 123
kkonganti@0 124 **Outputs**
kkonganti@0 125
kkonganti@0 126 The main output files are:
kkonganti@0 127
kkonganti@0 128 ::
kkonganti@0 129
kkonganti@0 130 - An tab-seperated file with possible matched annotations.
kkonganti@0 131 - A list of Lexmapr2 figures in PNG format.
kkonganti@0 132
kkonganti@0 133 ]]></help>
kkonganti@0 134 <citations>
kkonganti@0 135 <citation type="bibtex">
kkonganti@0 136 @misc{github,
kkonganti@0 137 author = {Penn, Kayla},
kkonganti@0 138 year = {2022},
kkonganti@0 139 title = {LexMapr2},
kkonganti@0 140 publisher = {GitHub},
kkonganti@0 141 journal = {GitHub repository},
kkonganti@0 142 url = {https://github.com/CFSAN-Biostatistics/LexMapr2}}
kkonganti@0 143 </citation>
kkonganti@0 144 <citation type="bibtex">
kkonganti@0 145 @misc{GalaxyToolWrapper,
kkonganti@0 146 author = {Konganti, Kranti},
kkonganti@2 147 year = {2022},
kkonganti@2 148 title = {Lexmapr2 Tool Wrapper for Galaxy},
kkonganti@2 149 journal = {GalaxyTrakr Tool repository},
kkonganti@2 150 url = {https://toolrepo.galaxytrakr.org/repository/browse_repository?id=e00d4fc8bba8b6c5}}
kkonganti@0 151 </citation>
kkonganti@0 152 </citations>
kkonganti@0 153 </tool>