# HG changeset patch
# User iuc
# Date 1726989990 0
# Node ID 3c19c84fbce247d121249f23a926508532c179de
# Parent  d9965e1430536a28298c4884ca6c41620324ec73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf commit 303002db06287fb25306020c4391626842f52162

diff -r d9965e143053 -r 3c19c84fbce2 fatovcf.xml
--- a/fatovcf.xml	Thu Sep 21 13:12:43 2023 +0000
+++ b/fatovcf.xml	Sun Sep 22 07:26:30 2024 +0000
@@ -48,7 +48,7 @@
     ]]></command>
     <inputs>
         <param name="in_fasta" format="fasta" type="data" label="FASTA Alignment" help="Must contain a series of sequences with different names and the same length. Both N and - are treated as missing information." />
-        
+
         <conditional name="ref_seq">
             <param name="refSeq" type="select" label="Determine reference sequence" help="Which sequence from the FASTA file should be used as the reference sequence.">
                 <option value="" selected="true">Use the first sequence as reference</option>
@@ -76,7 +76,7 @@
             <param argument="-windowSize" type="integer" min="0" value="0" label="Window size to mask bases" help="Mask any base for which there are at least -minAmbigWindow bases in a window of +-N bases around the base. Masking approach adapted from https://github.com/roblanf/sarscov2phylo/blob/master/scripts/mask_seq.py Use -windowSize=7 for same results. Default: 0" />
             <param argument="-minAmbigInWindow" type="integer" min="1" value="2" label="Minimum of ambiguous characters within the window given above" help="When -windowSize is provided, mask any base for which there are at least this many N, ambiguous or gap characters within the window. Default: 2" />
         </section>
-        
+
         <param argument="-includeNoAltN" type="boolean" truevalue="-includeNoAltN" falsevalue="" label="Include positions without defined ALT allele" help="Include base positions with no alternate alleles observed, but at least one N (missing base/no-call). Default: false" />
         <param argument="-minAc" type="integer" min="0" value="0" label="Minimum allele count" help="Ignore alternate alleles observed fewer than N times. Default: 0" />
         <param argument="-minAf" type="float" min="0.0" max="1.0" value="0.0" label="Minimum allele frequency" help="Ignore alternate alleles observed in less than F of non-N bases. Default: 0.0" />
@@ -136,7 +136,11 @@
 
 `faToVcf`_ is a tool to extract a VCF from a multi-sequence FASTA alignment.
 
-.. _faToVcf: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt 
+For implementation details see faToVcf's `source code`_.
+
+.. _faToVcf: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
+.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/utils/faToVcf/faToVcf.c
+
     ]]>    </help>
     <citations>
         <citation type="doi">10.1093/bib/bbs038</citation>