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annotate cfsan_lexmapr2.xml @ 13:bdccef316f65

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"planemo upload"
author kkonganti
date Thu, 15 Sep 2022 14:11:09 -0400
parents 530cafac56f9
children 89998b9b4d46
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@4 38 ./lexmapr2-input/$input.name
kkonganti@0 39 ]]></command>
kkonganti@0 40 <environment_variables>
kkonganti@0 41 <environment_variable name="NLTK_DATA">/tool/tool-data/cfsan_lexmapr2/0/nltk_data</environment_variable>
kkonganti@0 42 </environment_variables>
kkonganti@0 43 <inputs>
kkonganti@0 44 <param name="input" type="data" format="csv" label="Input CSV"
kkonganti@0 45 help="First row should be a header and first column should be sample names" />
kkonganti@2 46 <param name="embl_ont" type="text" optional="true"
kkonganti@2 47 label="User defined comma-separated EMBL Ontology short names" />
kkonganti@1 48 <conditional name="input_json">
kkonganti@1 49 <param name="json_is_set" type="boolean" label="Use User defined bins in JSON format?" />
kkonganti@1 50 <when value="true">
kkonganti@1 51 <param name="upload" type="data" format="json" label="User defined bins" />
kkonganti@1 52 </when>
kkonganti@1 53 <when value="false">
kkonganti@1 54 </when>
kkonganti@1 55 </conditional>
kkonganti@0 56 <param name="bins" truevalue="-b" type="boolean" checked="true"
kkonganti@0 57 label="Classify samples into default bins" help="Default: true"/>
kkonganti@0 58 <param name="graph" truevalue="-g" type="boolean" checked="true"
kkonganti@0 59 label="Visualize summary of mapping and binning" help="Default: true"/>
kkonganti@0 60 <param name="full" truevalue="-f" type="boolean" checked="false"
kkonganti@0 61 label="Generate full output format" help="Default: false"/>
kkonganti@0 62 <param name="no_ancestors" truevalue="-a" type="boolean" checked="false"
kkonganti@0 63 label="Remove ancestral terms from output" help="Default: false"/>
kkonganti@0 64 </inputs>
kkonganti@0 65 <outputs>
kkonganti@0 66 <data name="lexmapr2_output" format="tsv" label="Lexmapr2: On ${on_string}" from_work_dir="lexmapr2_output.tsv"/>
kkonganti@0 67 <collection name="plots" type="list" label="Lexmapr2: Plots on ${on_string}">
kkonganti@0 68 <discover_datasets pattern=".*\.png" ext="png" directory="lexmapr_figures"/>
kkonganti@0 69 </collection>
kkonganti@0 70 </outputs>
kkonganti@0 71 <tests>
kkonganti@0 72 <test expect_num_outputs="2">
kkonganti@0 73 <param name="input" value="test.csv"/>
kkonganti@0 74 </test>
kkonganti@0 75 </tests>
kkonganti@0 76 <help><![CDATA[
kkonganti@0 77
kkonganti@0 78 .. class:: infomark
kkonganti@0 79
kkonganti@0 80 **Purpose**
kkonganti@0 81
kkonganti@0 82 Lexmapr2 is a fork of Lexmapr (https://github.com/cidgoh/LexMapr) with the following added functionalitites:
kkonganti@0 83
kkonganti@0 84 ::
kkonganti@0 85
kkonganti@0 86 - pull ontology accession ids and definitions from EMBL-EBI via the API
kkonganti@0 87 - group mapped results by parent ontologies
kkonganti@0 88 - visualize mapping results
kkonganti@0 89
kkonganti@0 90 ----
kkonganti@0 91
kkonganti@0 92 .. class:: infomark
kkonganti@0 93
kkonganti@0 94 **Customization**
kkonganti@0 95
kkonganti@0 96 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 97
kkonganti@0 98 Example JSON format to use a bin titled 'ncbi_taxon':
kkonganti@0 99
kkonganti@0 100 ::
kkonganti@0 101
kkonganti@0 102 {
kkonganti@0 103 "ncbi_taxon":{
kkonganti@0 104 "Actinopterygii":"NCBITaxon_7898",
kkonganti@0 105 "Ecdysozoa":"NCBITaxon_1206794",
kkonganti@0 106 "Echinodermata":"NCBITaxon_7586",
kkonganti@0 107 "Fungi":"NCBITaxon_4751",
kkonganti@0 108 "Mammalia":"NCBITaxon_40674",
kkonganti@0 109 "Sauropsida":"NCBITaxon_8457",
kkonganti@0 110 "Spiralia":"NCBITaxon_2697495",
kkonganti@0 111 "Viridiplantae":"NCBITaxon_33090"
kkonganti@0 112 }
kkonganti@0 113 }
kkonganti@0 114
kkonganti@0 115 ----
kkonganti@0 116
kkonganti@0 117 .. class:: infomark
kkonganti@0 118
kkonganti@0 119 **Outputs**
kkonganti@0 120
kkonganti@0 121 The main output files are:
kkonganti@0 122
kkonganti@0 123 ::
kkonganti@0 124
kkonganti@0 125 - An tab-seperated file with possible matched annotations.
kkonganti@0 126 - A list of Lexmapr2 figures in PNG format.
kkonganti@0 127
kkonganti@0 128 ]]></help>
kkonganti@0 129 <citations>
kkonganti@0 130 <citation type="bibtex">
kkonganti@0 131 @misc{github,
kkonganti@0 132 author = {Penn, Kayla},
kkonganti@0 133 year = {2022},
kkonganti@0 134 title = {LexMapr2},
kkonganti@0 135 publisher = {GitHub},
kkonganti@0 136 journal = {GitHub repository},
kkonganti@0 137 url = {https://github.com/CFSAN-Biostatistics/LexMapr2}}
kkonganti@0 138 </citation>
kkonganti@0 139 <citation type="bibtex">
kkonganti@0 140 @misc{GalaxyToolWrapper,
kkonganti@0 141 author = {Konganti, Kranti},
kkonganti@2 142 year = {2022},
kkonganti@2 143 title = {Lexmapr2 Tool Wrapper for Galaxy},
kkonganti@2 144 journal = {GalaxyTrakr Tool repository},
kkonganti@2 145 url = {https://toolrepo.galaxytrakr.org/repository/browse_repository?id=e00d4fc8bba8b6c5}}
kkonganti@0 146 </citation>
kkonganti@0 147 </citations>
kkonganti@0 148 </tool>