Mercurial > repos > iuc > syri
annotate README.md @ 1:0d8128a8623e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit cb48fa8b0d1a3e4e2483b4b0ecea6011d4f71200
| author | iuc |
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| date | Mon, 28 Apr 2025 07:17:49 +0000 |
| parents | 27a56ecc88ee |
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| rev | line source |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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1 # SyRI Galaxy wrapper |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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2 |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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3 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. |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
iuc
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4 |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
iuc
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5 ## Minimap2 Galaxy Wrapper Compatibility |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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6 |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
iuc
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7 * When using minimap2 for generating alignments for syri, the minimum required Galaxy wrapper version is `2.28+galaxy1` |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
iuc
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8 * This version correctly adds the `--eqx` flag, which is required by SyRI to interpret alignment CIGAR strings |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
iuc
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9 |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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10 ## Accepted Alignment Inputs |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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11 |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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12 * For now alignments in `bam`, `sam` and `paf` are available as inputs |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
iuc
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13 * Delta file from mummer is currently not accepted |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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14 |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
iuc
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15 ## Sample name in output vcf |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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16 |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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17 * Users can add a sample name to add to output vcf. This is checked by regex |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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18 |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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19 ``` |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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20 <param argument="--samplename" name="sample_name" type="text" label="Sample name for the output VCF file. (default: sample)" optional="true"> |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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21 <validator type="regex" message="Invalid characters in sample name">^[a-zA-Z0-9\-_]+$</validator> |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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22 </param> |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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23 ``` |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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24 |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
iuc
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25 ## Empty Map IDs Output — Not an Error |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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26 |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
iuc
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27 * The output **Map IDs file** lists corresponding chromosomes between the reference and query genomes |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
iuc
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28 * SyRI only generates the output when the chromosome names differ between the two genomes. |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
iuc
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29 * If the chromosome names are identical, the file will be **absent or empty** — this is expected and not an error. |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
iuc
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30 |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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31 ## Exit codes |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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32 |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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33 * Any non zero |
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27a56ecc88ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri commit 85ece544d9a93ca2523c1ed44036b4cf7a4cfd57
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34 * Regex pattern `- ERROR -` in stderr/stdout |