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Request: add more to the Help section for dnadiff #6319

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jennaj opened this issue Sep 10, 2024 · 0 comments
Open

Request: add more to the Help section for dnadiff #6319

jennaj opened this issue Sep 10, 2024 · 0 comments

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@jennaj
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jennaj commented Sep 10, 2024

Tool toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0rc1+galaxy3

Add this content https://github.com/mummer4/mummer/blob/master/docs/dnadiff.README

To better clarify these outputs

**Output files:**
* report: Summary of alignments, differences and SNPs
* delta: Standard nucmer alignment output
* 1delta: 1-to-1 alignment from delta-filter -1
* mdelta: M-to-M alignment from delta-filter -m
* 1coords: 1-to-1 coordinates from show-coords -THrcl .1delta
* mcoords: M-to-M coordinates from show-coords -THrcl .mdelta
* snps: SNPs from show-snps -rlTHC .1delta
* rdiff: Classified ref breakpoints from show-diff -rH .mdelta
* qdiff: Classified qry breakpoints from show-diff -qH .mdelta

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