# HG changeset patch
# User richard-burhans
# Date 1724093115 0
# Node ID e9bf680c292b939d81c1b7736e986b98323b14be
# Parent  860e1f6f3de4540336e759685fc5ad77201d0dd5
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit a2f684fa36d99b0d8d03f2b802d08b56b8545bc6

diff -r 860e1f6f3de4 -r e9bf680c292b segalign.xml
--- a/segalign.xml	Mon Aug 12 15:41:13 2024 +0000
+++ b/segalign.xml	Mon Aug 19 18:45:15 2024 +0000
@@ -163,9 +163,46 @@
         </test>
     </tests>
     <help><![CDATA[
-    SegAlign is a scalable, GPU-accelerated system for computing pairwise WGA. SegAlign is based on the standard seed-filter-extend heuristic, in which the filtering stage dominates the runtime (e.g. 98% for human-mouse WGA), and is accelerated using GPU(s).
+SegAlign is a scalable, GPU-accelerated system for computing pairwise WGA. SegAlign is based on the standard seed-filter-extend heuristic, in which the filtering stage dominates the runtime (e.g. 98% for human-mouse WGA), and is accelerated using GPU(s). SegAlign was designed as a faster replacement for lastz pairwise aligner.
+
+**Using this tool**
+
+.. class:: warningmark
+
+This tool is the first part of a two-step process for generation of paiwrise alignments. The output of this tool is used as an input to **Batched LASTZ** tool. The *Batched LASTZ** can be found in the list of tool of this Galaxy instance.
+
+**What it does**
+
+SegAlign processes **Target** and **Query** sequences to identify highly similar regions where gapped extension will be performed to create actual alignments. The actual alignments are generated by **Batched LASTZ** that should be run on the output of this tool.
+
+.. class:: infomark
+
+Although this tool is only the first part of the alignment process all parameters related to generation of alignments are set **during this stage**.
+
+**Scoring Options**
+
+By default the HOXD70 substitution scores are used (from `Chiaromonte et al. 2002 <https://www.ncbi.nlm.nih.gov/pubmed/11928468>`_)::
 
-    https://github.com/gsneha26
+    bad_score          = X:-1000  # used for sub['X'][*] and sub[*]['X']
+    fill_score         = -100     # used when sub[*][*] is not defined
+    gap_open_penalty   =  400
+    gap_extend_penalty =   30
+
+         A     C     G     T
+    A   91  -114   -31  -123
+    C -114   100  -125   -31
+    G  -31  -125   100  -114
+    T -123   -31  -114    91
+
+Matrix can be supplied as an input to **Read the substitution scores** parameter in *Scoring* section. Substitution matrix can be inferred from your data using another LASTZ-based tool (LASTZ_D: Infer substitution scores).
+
+**Output Options**
+
+.. class:: infomark
+
+The final format in which alignmnets will be generated by **Batched LASTZ** are set here.
+
+The default output is a MAF alignment file. Other formats can be configured in *Output Options* section.  See LASTZ manual <https://lastz.github.io/lastz/#formats>`_ for description of possible formats.
     ]]></help>
     <expand macro="citations"/>
 </tool>