Mercurial > repos > iuc > text_to_wordmatrix

annotate text_to_wordmatrix.xml @ 0:0692d11af909 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
author iuc
date Wed, 24 Mar 2021 08:33:25 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
1 <tool id="text_to_wordmatrix" name="Text to wordmatrix" version="@VERSION@" license="MIT">
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
2 <description>by extracting most frequent words</description>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
3 <macros>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
5 </macros>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
6 <requirements>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
7 <requirement type="package" version="2.0.3">r-argparse</requirement>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
8 <requirement type="package" version="0.7.0">r-snowballc</requirement>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
9 <requirement type="package" version="0.3.6">r-pubmedwordcloud</requirement>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
10 <requirement type="package" version="1.2.0">r-semnetcleaner</requirement>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
11 <requirement type="package" version="0.9.3">r-textclean</requirement>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
12 <requirement type="package" version="1.5.3">r-stringi</requirement>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
13 <requirement type="package" version="1.4.0">r-stringr</requirement>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
14 </requirements>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
15 <command detect_errors="exit_code"><![CDATA[
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
16 Rscript
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
17 '${__tool_directory__}/text_to_wordmatrix.R'
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
18 --input '$input'
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
19 --output '$output'
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
20 --number '$number'
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
21 $remove_num
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
22 $lower_case
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
23 $remove_stopwords
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
24 $stemDoc
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
25 $plurals
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
26 ]]>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
27 </command>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
28 <inputs>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
29 <param argument="--input" type="data" format="tabular" label="Input file" />
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
30 <param argument="--number" type="integer" value="50" min="1" max="500" label="Number of most frequent words that should be extracted per row."/>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
31 <param argument="--remove_num" type="boolean" truevalue="--remove_num" falsevalue="" checked="false" label="Remove any numbers in text." />
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
32 <param argument="--lower_case" type="boolean" truevalue="" falsevalue="--lower_case" checked="true" label="Translate all characters are to lower case." />
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
33 <param argument="--remove_stopwords" type="boolean" truevalue="" falsevalue="--remove_stopwords" checked="true" label="Remove english stopwords" help="e.g. 'the' or 'not'" />
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
34 <param argument="--stemDoc" type="boolean" truevalue="--stemDoc" falsevalue="" checked="false" label="Apply Porter's stemming algorithm: collapsing words to a common root to aid comparison of vocabulary." />
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
35 <param argument="--plurals" type="boolean" truevalue="" falsevalue="--plurals" checked="true" label="Transform words in plural to their singular form." />
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
36 </inputs>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
37 <outputs>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
38 <data format="tabular" name="output" />
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
39 </outputs>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
40 <tests>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
41 <test>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
42 <param name="input" value="pubmed_by_queries_output_abstracts" ftype="tabular"/>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
43 <output name="output">
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
44 <assert_contents>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
45 <has_n_lines n="7"/>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
46 </assert_contents>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
47 </output>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
48 </test>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
49 <test>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
50 <param name="input" value="pubmed_by_queries_output_abstracts" ftype="tabular"/>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
51 <param name="remove_num" value="True"/>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
52 <param name="remove_stopwords" value="False"/>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
53 <param name="plurals" value="False"/>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
54 <output name="output">
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
55 <assert_contents>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
56 <has_n_lines n="7"/>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
57 </assert_contents>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
58 </output>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
59 </test>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
60 </tests>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
61 <help><![CDATA[
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
62
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
63 **What it does**
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
64
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
65 The tool extracts for each row the most frequent words from the text in columns starting with "ABSTRACT" or "TEXT. The extracted words from each row are united in one large binary matrix, with 0= word not frequently occurring in text of that row and 1= word frequently present in text of that row.
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
66
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
67 - Input table:
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
68
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
69 The output of "pubmed_by_queries" or "abstracts_by_pmids" tools, or a table with text in columns starting with "ABSTRACT" or "TEXT".
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
70
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
71 - Output table:
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
72
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
73 A binary matrix in that each column represents one of the extracted words.
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
74
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
75 -----
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
76
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
77 **Example**
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
78
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
79 - Input table:
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
80
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
81 | ABSTRACT_1 | ABSTRACT_2 | TEXT_1
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
82 | abcd def... | abcd def... | abcd def...
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
83 | abcd def... | abcd def... | abcd def...
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
84
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
85 - Extract of output table:
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
86
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
87 | chronic | seizure | child | channel | signaling | grin2a
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
88 | 1 | 1 | 1 | 1 | 1 | 1
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
89 | 0 | 1 | 0 | 1 | 0 | 1
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
90
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
91 ]]></help>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
92 <expand macro="citations"/>
0692d11af909 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
diff changeset
93 </tool>