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+++ b/macros.xml	Fri Apr 25 20:18:54 2025 +0000
@@ -0,0 +1,74 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.7.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/S13059-019-1911-0</citation>
+        </citations>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">syri</requirement>
+        </requirements>
+    </xml>
+    <xml name="help">
+        <help><![CDATA[
+SyRI (Synteny and Rearrangement Identifier)
+===========================================
+SyRI identifies structural rearrangements and local variations between two chromosome-level genome assemblies. It analyzes alignments from whole-genome alignment tools (like minimap2) and produces annotations of syntenic regions, inversions, translocations, duplications, SNPs, and indels.
+
+More Info
+---------
+ For more information please check the following links
+
+- Tool homepage: https://github.com/schneebergerlab/syri
+- Tutorial & documentation: https://schneebergerlab.github.io/syri/
+
+Inputs
+------
+
+- **Alignment file** (`BAM`, `SAM`, or `PAF`) from a whole-genome aligner like minimap2
+- **Reference genome** (FASTA)
+- **Query genome** (FASTA)
+ 
+Outputs
+-------
+
+- **Main output**: a TSV format file of annotated regions (synteny + rearrangements)
+- **Summary**: Statistics on structural events
+- **VCF**: Local variations (SNPs, indels)
+- **Map IDs**: Chromosome name mapping between reference and query (only populated if chromosome names differ)
+
+Notes:
+------
+
+- The **Map IDs file** lists corresponding chromosomes between the reference and query genomes. This file is **only generated** by SyRI when the chromosome names **differ** between the two genomes. If the chromosome names are identical, the file will be **empty** — this is expected and not an error.
+- When using **minimap2** to generate alignments for SyRI, the **minimum required Galaxy wrapper version is `2.28+galaxy1`**. This version correctly adds the `--eqx` flag, which is **required** by SyRI to interpret alignment CIGAR strings properly.
+
+Common Options
+--------------
+• **--seed**
+  Seed for generating random numbers.  
+  *Galaxy field:* “Seed for generating random numbers (default 1)”
+
+• **-f**  
+  Use the full list of alignments without filtering (default off).
+  *Galaxy field:* “Disable filtering of low-quality and small alignments”
+
+• **--samplename**
+  Sample name to be used in the output VCF file (default sample).  
+  *Galaxy field:* “Sample name for the output VCF file”
+
+• **--no-chrmatch**
+  Prevents automatic matching of chromosome IDs between the reference and query genomes.
+  *Galaxy field:* “Prevent automatic matching of chromosome IDs between genomes”
+
+Example Usage:
+--------------
+
+.. code-block:: bash
+
+   syri -c aln.bam -r ref.fasta -q qry.fasta -F B
+	]]></help>
+    </xml>
+</macros>