<macros>
    <token name="@TOOL_VERSION@">1.7.1</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>
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    <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>
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