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+# SyRI Galaxy wrapper
+
+Galaxy tool wrapper for [SyRI](https://github.com/schneebergerlab/syri): Synteny and Rearrangement Identifier. Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.
+
+## Minimap2 Galaxy Wrapper Compatibility
+
+* When using minimap2 for generating 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
+
+## Accepted Alignment Inputs
+
+* For now alignments in `bam`, `sam` and `paf` are available as inputs
+* Delta file from mummer is currently not accepted
+
+## Sample name in output vcf
+
+* Users can add a sample name to add to output vcf. This is checked by regex
+
+```
+  <param argument="--samplename" name="sample_name" type="text" label="Sample name for the output VCF file. (default: sample)" optional="true">
+    <validator type="regex" message="Invalid characters in sample name">^[a-zA-Z0-9\-_]+$</validator>
+  </param>
+```
+
+## Empty Map IDs Output — Not an Error
+
+* The output **Map IDs file** lists corresponding chromosomes between the reference and query genomes
+* SyRI only generates the output when the chromosome names differ between the two genomes.
+* If the chromosome names are identical, the file will be **absent or empty** — this is expected and not an error.
+
+## Exit codes
+
+* Any non zero
+* Regex pattern `- ERROR -` in stderr/stdout