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annotate cfsan_lexmapr2.xml @ 18:62b848017a6a

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"planemo upload"
author kkonganti
date Thu, 15 Sep 2022 14:48:03 -0400
parents b4ef74a844e6
children a2bf7a8b7bc9
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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 $__tool_directory__/lexmapr2.py --version</version_command>
kkonganti@0 15 <command detect_errors="exit_code"><![CDATA[
kkonganti@4 16 mkdir -p lexmapr2-input || exit 1;
kkonganti@13 17 ln -sf '/tool/tool-data/cfsan_lexmapr2/0/lexmapr' .;
kkonganti@4 18 ln -sf '$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@15 38 -o lexmapr2_output.tsv
kkonganti@17 39 ./lexmapr2-input/$input.name;
kkonganti@17 40 mv 'lexmapr_run.log' 'lexmapr2_run_log.txt' || exit 1;
kkonganti@0 41 ]]></command>
kkonganti@0 42 <environment_variables>
kkonganti@0 43 <environment_variable name="NLTK_DATA">/tool/tool-data/cfsan_lexmapr2/0/nltk_data</environment_variable>
kkonganti@14 44 <environment_variable name="PYTHONPATH">/tool/tool-data/cfsan_lexmapr2/0</environment_variable>
kkonganti@0 45 </environment_variables>
kkonganti@0 46 <inputs>
kkonganti@0 47 <param name="input" type="data" format="csv" label="Input CSV"
kkonganti@0 48 help="First row should be a header and first column should be sample names" />
kkonganti@2 49 <param name="embl_ont" type="text" optional="true"
kkonganti@2 50 label="User defined comma-separated EMBL Ontology short names" />
kkonganti@1 51 <conditional name="input_json">
kkonganti@1 52 <param name="json_is_set" type="boolean" label="Use User defined bins in JSON format?" />
kkonganti@1 53 <when value="true">
kkonganti@1 54 <param name="upload" type="data" format="json" label="User defined bins" />
kkonganti@1 55 </when>
kkonganti@1 56 <when value="false">
kkonganti@1 57 </when>
kkonganti@1 58 </conditional>
kkonganti@0 59 <param name="bins" truevalue="-b" type="boolean" checked="true"
kkonganti@0 60 label="Classify samples into default bins" help="Default: true"/>
kkonganti@0 61 <param name="graph" truevalue="-g" type="boolean" checked="true"
kkonganti@0 62 label="Visualize summary of mapping and binning" help="Default: true"/>
kkonganti@15 63 <param name="full" truevalue="-f" type="boolean" checked="true"
kkonganti@15 64 label="Generate full output format" help="Default: true"/>
kkonganti@0 65 <param name="no_ancestors" truevalue="-a" type="boolean" checked="false"
kkonganti@0 66 label="Remove ancestral terms from output" help="Default: false"/>
kkonganti@0 67 </inputs>
kkonganti@0 68 <outputs>
kkonganti@16 69 <data name="lexmapr2_output" format="tsv" label="Lexmapr2: Results On ${on_string}" from_work_dir="lexmapr2_output.tsv"/>
kkonganti@0 70 <collection name="plots" type="list" label="Lexmapr2: Plots on ${on_string}">
kkonganti@18 71 <discover_datasets pattern="(?P&lt;designation&gt;.+)" format="png" directory="lexmapr_figures"/>
kkonganti@0 72 </collection>
kkonganti@17 73 <data name="lexmapr2_log" format="txt" label="Lexmapr2: Log On ${on_string}" from_work_dir="lexmapr2_run_log.txt"/>
kkonganti@0 74 </outputs>
kkonganti@0 75 <tests>
kkonganti@0 76 <test expect_num_outputs="2">
kkonganti@0 77 <param name="input" value="test.csv"/>
kkonganti@0 78 </test>
kkonganti@0 79 </tests>
kkonganti@0 80 <help><![CDATA[
kkonganti@0 81
kkonganti@0 82 .. class:: infomark
kkonganti@0 83
kkonganti@0 84 **Purpose**
kkonganti@0 85
kkonganti@0 86 Lexmapr2 is a fork of Lexmapr (https://github.com/cidgoh/LexMapr) with the following added functionalitites:
kkonganti@0 87
kkonganti@0 88 ::
kkonganti@0 89
kkonganti@0 90 - pull ontology accession ids and definitions from EMBL-EBI via the API
kkonganti@0 91 - group mapped results by parent ontologies
kkonganti@0 92 - visualize mapping results
kkonganti@0 93
kkonganti@0 94 ----
kkonganti@0 95
kkonganti@0 96 .. class:: infomark
kkonganti@0 97
kkonganti@0 98 **Customization**
kkonganti@0 99
kkonganti@0 100 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@0 101
kkonganti@0 102 Example JSON format to use a bin titled 'ncbi_taxon':
kkonganti@0 103
kkonganti@0 104 ::
kkonganti@0 105
kkonganti@0 106 {
kkonganti@0 107 "ncbi_taxon":{
kkonganti@0 108 "Actinopterygii":"NCBITaxon_7898",
kkonganti@0 109 "Ecdysozoa":"NCBITaxon_1206794",
kkonganti@0 110 "Echinodermata":"NCBITaxon_7586",
kkonganti@0 111 "Fungi":"NCBITaxon_4751",
kkonganti@0 112 "Mammalia":"NCBITaxon_40674",
kkonganti@0 113 "Sauropsida":"NCBITaxon_8457",
kkonganti@0 114 "Spiralia":"NCBITaxon_2697495",
kkonganti@0 115 "Viridiplantae":"NCBITaxon_33090"
kkonganti@0 116 }
kkonganti@0 117 }
kkonganti@0 118
kkonganti@0 119 ----
kkonganti@0 120
kkonganti@0 121 .. class:: infomark
kkonganti@0 122
kkonganti@0 123 **Outputs**
kkonganti@0 124
kkonganti@0 125 The main output files are:
kkonganti@0 126
kkonganti@0 127 ::
kkonganti@0 128
kkonganti@0 129 - An tab-seperated file with possible matched annotations.
kkonganti@0 130 - A list of Lexmapr2 figures in PNG format.
kkonganti@0 131
kkonganti@0 132 ]]></help>
kkonganti@0 133 <citations>
kkonganti@0 134 <citation type="bibtex">
kkonganti@0 135 @misc{github,
kkonganti@0 136 author = {Penn, Kayla},
kkonganti@0 137 year = {2022},
kkonganti@0 138 title = {LexMapr2},
kkonganti@0 139 publisher = {GitHub},
kkonganti@0 140 journal = {GitHub repository},
kkonganti@0 141 url = {https://github.com/CFSAN-Biostatistics/LexMapr2}}
kkonganti@0 142 </citation>
kkonganti@0 143 <citation type="bibtex">
kkonganti@0 144 @misc{GalaxyToolWrapper,
kkonganti@0 145 author = {Konganti, Kranti},
kkonganti@2 146 year = {2022},
kkonganti@2 147 title = {Lexmapr2 Tool Wrapper for Galaxy},
kkonganti@2 148 journal = {GalaxyTrakr Tool repository},
kkonganti@2 149 url = {https://toolrepo.galaxytrakr.org/repository/browse_repository?id=e00d4fc8bba8b6c5}}
kkonganti@0 150 </citation>
kkonganti@0 151 </citations>
kkonganti@0 152 </tool>