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