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+++ b/aoptk_publication_tracker.xml	Wed Feb 04 09:43:20 2026 +0000
@@ -0,0 +1,112 @@
+<tool id="aoptk_publication_tracker" name="aoptk publication tracker" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.1" license="MIT">
+    <description>Tool to track publications.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <requirements>
+        <expand macro="requirements"/>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$read' 'read.${read.ext}' &&
+        ln -s '$master' 'master.${master.ext}' &&
+        publication-tracker
+            --read 'read.${read.ext}'
+            --master 'master.${master.ext}'
+            --code '$code'
+            --query '$query'
+            --database '$literature_database'
+            --outdir .
+            \${EMAIL:+--email \$EMAIL}
+    ]]></command>
+
+    <inputs>
+        <expand macro="inputs"/>
+        <param argument="--code" type="text" value="" label="Your search code" help="Type your search code. E.g., 1.1. or 1.2.1.">
+            <sanitizer invalid_char="">
+                <valid initial="string.digits">
+                    <add value="." />
+                 </valid>
+            </sanitizer>
+            <validator type="regex">^\d+(\.\d+)*\.?$</validator>
+        </param>
+        <param argument="--read" type="data" format="xlsx" label="Your database of read publications" help="Your database of read publications. Column id must be present." />
+        <param argument="--master" type="data" format="xlsx" label="Your master table" help="Your master table. Columns ID and Search code must be present." />
+
+    </inputs>
+
+    <outputs>
+        <data name="updated_master_table" format="xlsx" from_work_dir="updated_master_table.xlsx" label="Updated master table" />
+        <data name="to_read" format="xlsx" from_work_dir="to_read.xlsx" label="To read" />
+    </outputs>
+
+    <tests>
+        <!-- Hint: You can use [ctrl+alt+t] after defining the inputs/outputs to auto-scaffold some basic test cases. -->
+        <test>
+           <param name="query" value="hepg2 thioacetamide"/>
+           <param name="code" value="1.1.1."/>
+           <param name="literature_database" value="pubmed"/>
+           <param name="read" value="read_test.xlsx"/>
+           <param name="master" value="master_test.xlsx"/>
+           <output name="to_read" file="read1.xlsx" compare="sim_size" delta="100"/>
+        </test>
+        <test>
+           <param name="query" value="hepg2 heparg thioacetamide spheroid"/>
+           <param name="code" value="1.2.1."/>
+           <param name="literature_database" value="europepmc"/>
+           <param name="read" value="read_test.xlsx"/>
+           <param name="master" value="master_test.xlsx"/>
+           <output name="to_read" file="read2.xlsx" compare="sim_size" delta="100"/>
+        </test>
+        <test>
+           <param name="query" value="lx-2 col1a1"/>
+           <param name="code" value="3.1."/>
+           <param name="literature_database" value="pubmed"/>
+           <param name="read" value="read_test.xlsx"/>
+           <param name="master" value="master_test.xlsx"/>
+           <output name="updated_master_table" file="updated_master_table.xlsx" compare="sim_size" delta="100"/>
+           <output name="to_read" file="read3.xlsx" compare="sim_size" delta="100"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Publication-Tracker
+===================
+Publication-Tracker allows you to filter for publications which you have read already and automatically update search codes in your master table.
+
+How It Works
+------------
+- Provide your email address — required by NCBI.
+- Enter a search term — exactly as you would in PubMed or Europe PMC.
+- Choose a database — PubMed or Europe PMC.
+- Assign a search code — a unique identifier for your search, e.g., 1.1. or 1.2.1. Maintain rationale behind this search code in Search-code table.
+- Upload database of read publications — an Excel file with a column named `id` containing publications you have already read.
+- Upload master table — an Excel file with columns `ID` and `Search code`. This is where you will map your publications to their corresponding search codes.
+- Master table with updated search codes will be generated.
+- File with yet not read publications will be generated.
+
+Output Files
+------------
+
+- **Publications to read:** List of publications that match your search term and have not been read yet.
+- **Updated master table:** Master table with updated search codes.
+
+Notes on Creating Database of Read Publications and Master Table
+----------------------------------------------------------------
+
+- **Database of read publications:** Must be an Excel file with a column named `id` containing the PubMed IDs (or other identifier if not available) of the publications you have read.
+- **Master table:** Must be an Excel file with columns `ID` (PubMed ID or other identifier) and `Search code`. This table will be updated with new search codes.
+
+How to cite
+===========
+
+If you use Publication-Tracker in your research, please cite [DOI TBA]. 
+Publication-Tracker was originally developed for the purposes of this publication.
+
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btp163</citation>
+    </citations>
+</tool>
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