--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/openalex.xml	Sat May 31 12:25:24 2025 +0000
@@ -0,0 +1,88 @@
+<tool id="openalex_explorer" name="OpenAlex explorer" version="0.1.0+galaxy0" profile="23.1">
+    <description>Fetch citing papers from OpenAlex using DOI, openAlex ID, or title</description>
+    <requirements>
+        <requirement type="package" version="3.10">python</requirement>
+        <requirement type="package" version="2.31.0">requests</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+python3 '$__tool_directory__/openalex_fetch.py'
+$input_type '$identifier'
+--max-citations '$max_citations'
+$download_pdfs
+]]></command>
+    <inputs>
+        <param name="input_type" type="select" label="Input type" help="Select whether the identifier is an OpenAlex ID, DOI, or Title">
+            <option value="--doi" selected="true">DOI</option>
+            <option value="--id">OpenAlex ID</option>
+            <option value="--title">Title</option>
+        </param>
+        <param name="identifier" type="text" label="Identifier" help="Enter the OpenAlex ID, DOI, or Title depending on your selection above"/>
+        <param name="download_pdfs" type="boolean" truevalue="--download" falsevalue="" label="Download available OA PDFs?" value="false"/>
+        <param name="max_citations" type="select" label="Max citing papers to fetch" help="Limit the number of citing papers to fetch">
+            <option value="10">10</option>
+            <option value="20">20</option>
+            <option value="50" selected="true">50</option>
+            <option value="100">100</option>
+            <option value="all">All</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="summary_out" format="txt" label="Citation Summary" from_work_dir="summary.txt"/>
+        <data name="tsv_out" format="tabular" label="Citing Papers TSV" from_work_dir="citing_papers.tsv"/>
+        <collection name="pdf_outputs" label="Downloaded PDFs" type="list" format="pdf">
+            <discover_datasets pattern="__designation_and_ext__" directory="downloads"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_type" value="--id"/>
+            <param name="identifier" value="W4398182689"/>
+            <param name="max_citations" value="10"/>
+            <param name="download_pdfs" value="false"/>
+            <output name="summary_out" file="expected_summary.txt"/>
+            <output name="tsv_out" file="expected_citing_papers.tsv"/>
+        </test>
+        <test>
+            <param name="input_type" value="--doi"/>
+            <param name="identifier" value="10.1093/nar/gkae410"/>
+            <param name="max_citations" value="50"/>
+            <param name="download_pdfs" value="false"/>
+            <output name="summary_out" file="expected_summary_doi.txt"/>
+            <output name="tsv_out" file="expected_citing_papers_doi.tsv"/>
+        </test>
+        <test>
+            <param name="input_type" value="--title"/>
+            <param name="identifier" value="The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update"/>
+            <param name="max_citations" value="50"/>
+            <param name="download_pdfs" value="false"/>
+            <output name="summary_out" file="expected_summary_title.txt"/>
+            <output name="tsv_out" file="expected_citing_papers_title.tsv"/>
+        </test>
+        <test>
+            <param name="input_type" value="--id"/>
+            <param name="identifier" value="W2088676066"/>
+            <param name="max_citations" value="10"/>
+            <param name="download_pdfs" value="true"/>
+            <output name="summary_out" file="expected_summary_wddownload.txt"/>
+            <output name="tsv_out" file="expected_citing_papers_wddownload.tsv"/>
+            <output_collection name="pdf_outputs" type="list" count="1">
+                <!-- Also working with the line below but I guess count check would be suffice -->
+                <!-- <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"/> -->
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+    This tool fetches citing papers from OpenAlex for a paper specified by OpenAlex ID, DOI, or Title.
+
+        You can optionally download available Open Access PDFs.
+
+        **Outputs:**
+
+        - summary.txt: summary of total, OA, and closed access citing papers
+
+        - citing_papers.tsv: list of citing papers with details (title, DOI, OA)
+    ]]></help>
+    <citations>
+        <citation type="doi">10.48550/arXiv.2205.01833</citation>
+    </citations>
+</tool>