Mercurial > repos > iuc > openalex_explorer
annotate openalex.xml @ 0:1678b5f97915 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
| author | iuc |
|---|---|
| date | Sat, 31 May 2025 12:25:24 +0000 |
| parents | |
| children |
| rev | line source |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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1 <tool id="openalex_explorer" name="OpenAlex explorer" version="0.1.0+galaxy0" profile="23.1"> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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2 <description>Fetch citing papers from OpenAlex using DOI, openAlex ID, or title</description> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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3 <requirements> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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4 <requirement type="package" version="3.10">python</requirement> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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5 <requirement type="package" version="2.31.0">requests</requirement> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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6 </requirements> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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changeset
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7 <command detect_errors="exit_code"><![CDATA[ |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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changeset
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8 python3 '$__tool_directory__/openalex_fetch.py' |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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9 $input_type '$identifier' |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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10 --max-citations '$max_citations' |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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11 $download_pdfs |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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changeset
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12 ]]></command> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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13 <inputs> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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14 <param name="input_type" type="select" label="Input type" help="Select whether the identifier is an OpenAlex ID, DOI, or Title"> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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15 <option value="--doi" selected="true">DOI</option> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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16 <option value="--id">OpenAlex ID</option> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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17 <option value="--title">Title</option> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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18 </param> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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19 <param name="identifier" type="text" label="Identifier" help="Enter the OpenAlex ID, DOI, or Title depending on your selection above"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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20 <param name="download_pdfs" type="boolean" truevalue="--download" falsevalue="" label="Download available OA PDFs?" value="false"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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21 <param name="max_citations" type="select" label="Max citing papers to fetch" help="Limit the number of citing papers to fetch"> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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22 <option value="10">10</option> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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23 <option value="20">20</option> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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24 <option value="50" selected="true">50</option> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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changeset
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25 <option value="100">100</option> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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26 <option value="all">All</option> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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27 </param> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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28 </inputs> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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29 <outputs> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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30 <data name="summary_out" format="txt" label="Citation Summary" from_work_dir="summary.txt"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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31 <data name="tsv_out" format="tabular" label="Citing Papers TSV" from_work_dir="citing_papers.tsv"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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32 <collection name="pdf_outputs" label="Downloaded PDFs" type="list" format="pdf"> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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changeset
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33 <discover_datasets pattern="__designation_and_ext__" directory="downloads"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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changeset
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34 </collection> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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35 </outputs> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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36 <tests> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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37 <test> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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38 <param name="input_type" value="--id"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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changeset
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39 <param name="identifier" value="W4398182689"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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40 <param name="max_citations" value="10"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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41 <param name="download_pdfs" value="false"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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42 <output name="summary_out" file="expected_summary.txt"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
diff
changeset
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43 <output name="tsv_out" file="expected_citing_papers.tsv"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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changeset
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44 </test> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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45 <test> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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changeset
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46 <param name="input_type" value="--doi"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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changeset
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47 <param name="identifier" value="10.1093/nar/gkae410"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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changeset
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48 <param name="max_citations" value="50"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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changeset
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49 <param name="download_pdfs" value="false"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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changeset
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50 <output name="summary_out" file="expected_summary_doi.txt"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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changeset
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51 <output name="tsv_out" file="expected_citing_papers_doi.tsv"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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52 </test> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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53 <test> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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54 <param name="input_type" value="--title"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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55 <param name="identifier" value="The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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56 <param name="max_citations" value="50"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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changeset
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57 <param name="download_pdfs" value="false"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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58 <output name="summary_out" file="expected_summary_title.txt"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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changeset
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59 <output name="tsv_out" file="expected_citing_papers_title.tsv"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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60 </test> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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61 <test> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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62 <param name="input_type" value="--id"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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63 <param name="identifier" value="W2088676066"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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64 <param name="max_citations" value="10"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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65 <param name="download_pdfs" value="true"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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66 <output name="summary_out" file="expected_summary_wddownload.txt"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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67 <output name="tsv_out" file="expected_citing_papers_wddownload.tsv"/> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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68 <output_collection name="pdf_outputs" type="list" count="1"> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
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69 <!-- Also working with the line below but I guess count check would be suffice --> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
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70 <!-- <element name="NAC-MYB-based transcriptional regulation of secondary cell wall biosynthesis in land plants" file="downloads/NAC-MYB-based transcriptional regulation of secondary cell wall biosynthesis in land plants.pdf"/> --> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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71 </output_collection> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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72 </test> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
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73 </tests> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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74 <help><![CDATA[ |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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75 This tool fetches citing papers from OpenAlex for a paper specified by OpenAlex ID, DOI, or Title. |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
parents:
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76 |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
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77 You can optionally download available Open Access PDFs. |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
iuc
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78 |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
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79 **Outputs:** |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
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80 |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
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81 - summary.txt: summary of total, OA, and closed access citing papers |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
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82 |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
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83 - citing_papers.tsv: list of citing papers with details (title, DOI, OA) |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
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84 ]]></help> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
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85 <citations> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
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86 <citation type="doi">10.48550/arXiv.2205.01833</citation> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
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87 </citations> |
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1678b5f97915
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/openalex commit 7bac5b8acf6091006591be468a252e57793db4d8
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88 </tool> |