--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tb_profiler_collate.xml	Tue Oct 21 10:24:27 2025 +0000
@@ -0,0 +1,73 @@
+<tool id="tb_profiler_collate" name="TB-Profiler Collate" version="@TOOL_VERSION@+galaxy1" profile="21.05">
+  <description>Combines multiple TB-Profiler JSON reports into summary and variants reports</description>
+
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+
+  <requirements>
+    <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement>
+  </requirements>
+
+  <expand macro="version_command"/>
+
+  <command detect_errors="exit_code"><![CDATA[
+    #for $dataset in $input_files
+        python '$__tool_directory__/replace_id_field_with_element_id.py' '$dataset' '$dataset.element_identifier' &&
+    #end for
+
+    tb-profiler collate --dir .
+  ]]></command>
+
+  <inputs>
+    <param type="data_collection" name="input_files" label="TB-Profiler JSON Reports" collection_type="list" format="json" help="Enter a list of TB-Profiler JSON reports to collate."/>
+  </inputs>
+
+  <outputs>  
+    <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string}: Summary Report (tabular)" from_work_dir="tbprofiler.txt">
+        <actions>
+            <action name="column_names" type="metadata" default="sample,main_lineage,sub_lineage,spoligotype,drtype,target_median_depth,pct_reads_mapped,num_reads_mapped,num_dr_variants,num_other_variants,rifampicin,isoniazid,ethambutol,pyrazinamide,moxifloxacin,levofloxacin,bedaquiline,delamanid,pretomanid,linezolid,streptomycin,amikacin,kanamycin,capreomycin,clofazimine,ethionamide,para-aminosalicylic_acid,cycloserine"/>
+            <action type="metadata" name="detect_metadata"/>
+        </actions>
+    </data>
+    <data name="output_csv" format="csv" label="${tool.name} on ${on_string}: Variants Report (CSV)" from_work_dir="tbprofiler.variants.csv"/>
+    <data name="output_variants" format="txt" label="${tool.name} on ${on_string}: Variants Report (TXT)" from_work_dir="tbprofiler.variants.txt"/>
+  </outputs>
+
+  <tests>
+      <test expect_num_outputs="3">
+          <param name="input_files">
+              <collection type="list">
+                  <element name="ERR2510682" value="ERR2510682.results.json" ftype="json"/>
+              </collection>
+          </param>
+
+          <output name="output_tabular" file="tbprofiler_test_1_sample.txt" ftype="tabular"/>
+          <output name="output_csv" file="tbprofiler_test_1_sample.variants.csv"/>
+          <output name="output_variants" file="tbprofiler_test_1_sample.variants.txt"/>
+      </test>
+  </tests>
+
+  <help><![CDATA[
+  TB-Profiler Collate Tool
+
+  This tool combines multiple TB-Profiler JSON reports into consolidated outputs, summarizing lineage, antimicrobial resistance (AMR) profiles, and variants across samples.
+
+  Inputs
+  - A collection of TB-Profiler JSON reports generated from individual samples.
+
+  Outputs
+  1. Summary Report (tbprofiler.txt): Overview of sample lineages and AMR predictions.
+  2. Variants CSV (tbprofiler.variants.csv): Table of identified variants across all samples.
+  3. Variants Text (tbprofiler.variants.txt): Text file of variant details for quick inspection.
+
+  Usage Notes
+  - Ensure all input JSON files are valid TB-Profiler outputs.
+
+  ]]></help>
+
+  <citations>
+      <citation type="doi">10.1186/s13073-019-0676-5</citation>
+  </citations>
+
+</tool>