Mercurial > repos > kkonganti > cfsan_lexmapr2

comparison cfsan_lexmapr2.xml @ 3:be95a7ce968a tip

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"planemo upload"
author kkonganti
date Tue, 13 Sep 2022 11:32:24 -0400
parents f5c39d0447be
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1:5244e7465767 3:be95a7ce968a
26 -u "$in_json" 26 -u "$in_json"
27 #end if 27 #end if
28 #end for 28 #end for
29 ]]></command> 29 ]]></command>
30 <environment_variables> 30 <environment_variables>
31 <environment_variable name="NLTK_DATA">$__tool_directory__/nltk_data</environment_variable> 31 <environment_variable name="NLTK_DATA">/tool/tool-data/cfsan_lexmapr2/0/nltk_data</environment_variable>
32 </environment_variables> 32 </environment_variables>
33 <inputs> 33 <inputs>
34 <param name="input" type="data" format="csv" label="Input CSV" 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" /> 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" 36 <param name="input_json" type="data" format="json" optional="true"
69 69
70 - pull ontology accession ids and definitions from EMBL-EBI via the API 70 - pull ontology accession ids and definitions from EMBL-EBI via the API
71 - group mapped results by parent ontologies 71 - group mapped results by parent ontologies
72 - visualize mapping results 72 - visualize mapping results
73 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 }
74 98
75 ---- 99 ----
76 100
77 .. class:: infomark 101 .. class:: infomark
78 102
80 104
81 The main output files are: 105 The main output files are:
82 106
83 :: 107 ::
84 108
85 - An tab-seperated file with matched annotations. 109 - An tab-seperated file with possible matched annotations.
86 - A list of Lexmapr2 figures in PNG format. 110 - A list of Lexmapr2 figures in PNG format.
87
88
89 111
90 ]]></help> 112 ]]></help>
91 <citations> 113 <citations>
92 <citation type="bibtex"> 114 <citation type="bibtex">
93 @misc{github, 115 @misc{github,