Mercurial > repos > iuc > abstracts_by_pmids

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
author iuc
date Wed, 24 Mar 2021 08:32:54 +0000
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ff904894ccaa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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1 <tool id="abstracts_by_pmids" name="Get PubMed abstracts" version="@VERSION@" license="MIT">
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2 <description>by PMID IDs</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="2.0.3">r-argparse</requirement>
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8 <requirement type="package" version="0.2.3">r-reutils</requirement>
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9 <requirement type="package" version="2.13">r-easypubmed</requirement>
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10 <requirement type="package" version="0.9.3">r-textclean</requirement>
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11 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
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13 Rscript
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14 '${__tool_directory__}/abstracts_by_pmids.R'
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15 --input '$input'
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16 --output '$output'
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param argument="--input" type="data" format="tabular" label="Input file with PMID IDs" />
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21 </inputs>
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22 <outputs>
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23 <data format="tabular" name="output" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="input" value="pubmed_by_queries_output" ftype="tabular"/>
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28 <output name="output">
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29 <assert_contents>
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30 <has_n_lines n="7"/>
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31 </assert_contents>
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32 </output>
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33 </test>
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34 </tests>
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35 <help><![CDATA[
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36
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37 **What it does**
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38
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39 This tool retrieves for all PMIDs in each row of a table the according abstracts and saves them in additional columns.
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40
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41 -----
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43 **Example**
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44
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45 - Input file:
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46 Table with rows representing biomedical entities and columns containing the corresponding PMIDs. The names of the PMID columns should start with “PMID\_” (e.g., “PMID_1”, “PMID_2” etc.).
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47
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48 | PMID_1 | PMID_2 | PMID_2
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49 | 33565071 | 33531663 | 33528079
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50 | 33377604 | 33334860 | 33277917
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51
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52 - Output file:
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53 A table with additional columns containing the abstract texts.
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54
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55 | PMID_1 | PMID_2 | PMID_2 | ABSTRACT_1 | ABSTRACT_3 | ABSTRACT_3
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56 | 33565071 | 33531663 | 33528079 | abc def... | abc def... | abc def...
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57 | 33377604 | 33334860 | 33277917 | abc def... | abc def... | abc def...
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58
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59 ]]></help>
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60 <expand macro="citations"/>
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61 </tool>