Mercurial > repos > iuc > pmids_to_pubtator_matrix
annotate pmids_to_pubtator_matrix.xml @ 0:69714f06f18b draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
author | iuc |
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date | Wed, 24 Mar 2021 08:33:56 +0000 |
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0
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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1 <tool id="pmids_to_pubtator_matrix" name="PMIDs to PubTator" version="@VERSION@" license="MIT"> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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2 <description>binary matrix</description> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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3 <macros> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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4 <import>macros.xml</import> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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5 </macros> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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6 <requirements> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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7 <requirement type="package" version="2.0.3">r-argparse</requirement> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
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8 <requirement type="package" version="1.4.0">r-stringr</requirement> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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9 <requirement type="package" version="1.98_1.2">r-rcurl</requirement> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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10 <requirement type="package" version="1.5.3">r-stringi</requirement> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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11 </requirements> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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12 <command detect_errors="exit_code"><![CDATA[ |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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13 Rscript |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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14 '${__tool_directory__}/pmids_to_pubtator_matrix.R' |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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15 --input '$input' |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
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16 --output '$output' |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
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17 --number '$number' |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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18 $byid |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
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19 --categories |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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20 #for $category in $categories: |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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21 '$category' |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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22 #end for |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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23 ]]> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
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24 </command> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
parents:
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25 <inputs> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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26 <param argument="--input" type="data" format="tabular" label="Input file with PMID IDs" /> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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27 <param argument="--categories" type="select" label="categories" multiple="true" display="checkboxes"> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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28 <option value="Gene">Genes</option> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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29 <option value="Disease">Diseases</option> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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30 <option value="Mutation">Mutations</option> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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31 <option value="Chemical">Chemicals</option> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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32 <option value="Species">Species</option> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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33 </param> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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34 <param argument="--byid" label="If you want to find common gene IDs / mesh IDs instead of specific scientific terms." name="byid" type="boolean" truevalue="--byid" falsevalue="" help="byid" checked="false"/> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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35 <param argument="--number" label="Number of most frequent terms/IDs to extract." name="number" optional="true" type="integer" help="number" value="50"/> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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36 </inputs> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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37 <outputs> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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38 <data format="tabular" name="output" /> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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39 </outputs> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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40 <tests> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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41 <test> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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42 <param name="input" value="pubmed_by_queries_output" ftype="tabular"/> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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43 <param name="categories" value="Gene,Mutation"/> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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44 <output name="output"> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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45 <assert_contents> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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46 <has_n_lines n="7"/> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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47 </assert_contents> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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48 </output> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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49 </test> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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50 <test> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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51 <param name="input" value="pubmed_by_queries_output" ftype="tabular"/> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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52 <param name="categories" value="Gene,Disease"/> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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53 <param name="byid" value="True"/> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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54 <output name="output"> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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55 <assert_contents> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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56 <has_n_lines n="7"/> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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57 </assert_contents> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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58 </output> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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59 </test> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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60 <test> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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61 <param name="input" value="pubmed_by_queries_output" ftype="tabular"/> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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62 <param name="categories" value="Gene,Disease"/> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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63 <param name="number" value="5"/> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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64 <output name="output"> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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65 <assert_contents> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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66 <has_n_lines n="7"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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67 </assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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68 </output> |
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69 </test> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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70 </tests> |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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71 <help><![CDATA[ |
69714f06f18b
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72 |
69714f06f18b
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73 **What it does** |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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74 |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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75 The tool uses all PMIDs per row and extracts "Gene", "Disease", "Mutation", "Chemical" and "Species" terms of the corresponding abstracts, |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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76 using PubTator annotations. The user can choose from which categories terms should be extracted. The extracted terms are united in one |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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77 large binary matrix, with 0= term not present in abstracts of that row and 1= term present in abstracts of that row. |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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78 The user can decide if the scientific terms should be extracted and used as they are or if they should be grouped by their |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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79 geneIDs/ meshIDs (several terms are often grouped into one ID). The the user can specify a number of most frequent words to extract per row. |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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80 |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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81 - Input file: |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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82 |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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83 Output of 'abstracts_by_pmids' tool, or tab-delimited table with columns containing PMIDs. |
69714f06f18b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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84 The names of the PMID columns should start with "PMID", e.g. "PMID_1", "PMID_2" etc. |
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85 |
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86 - Output file: |
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87 |
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88 Binary matrix in that each column represents one of the extracted terms. |
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89 |
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90 ----- |
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91 |
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92 **Example** |
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93 |
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94 - Input table: |
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95 |
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96 | PMID_1 | PMID_2 | PMID_2 |
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97 | 33565071 | 33531663 | 33528079 |
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98 | 33377604 | 33334860 | 33277917 |
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99 |
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100 - Extract of output table: |
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101 |
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102 | egfr | hormone | tp53 | scn8a | cacna1a | grin2a |
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103 | 1 | 0 | 1 | 0 | 1 | 0 |
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104 | 1 | 1 | 1 | 1 | 0 | 1 |
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105 |
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106 |
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107 ]]></help> |
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108 <expand macro="citations"/> |
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109 </tool> |