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comparison cfsan_lexmapr2.xml @ 0:91438d32ed58

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