# HG changeset patch
# User kkonganti
# Date 1721074619 14400
# Node ID 78a02e8cb092e66add1996f032c9f3983ce289de
# Parent  a5f31c44f8c901ab799cce0f5413072d2e91ab7d
planemo upload

diff -r a5f31c44f8c9 -r 78a02e8cb092 cfsan_cronology.xml
--- a/cfsan_cronology.xml	Mon Jul 15 16:11:44 2024 -0400
+++ b/cfsan_cronology.xml	Mon Jul 15 16:16:59 2024 -0400
@@ -75,7 +75,7 @@
         <param name="refgenome" optional="true" value="GCF_003516125" type="text"
                 label="NCBI reference genome accession"
                 help="Is the reference genome other than Cronobacter sakazakii? Reference genome FASTA is used as a model for gene prediction. DO NOT ENTER THE DECIMAL PART (Ex: GCF_003516125.1)." />
-        <param name="tuspy_n" optional="true" value="2" type="integer" label="Enter the number of top unique hits to retain after initial MASH screen step"
+        <param name="tuspy_n" optional="true" value="5" type="integer" label="Enter the number of top unique hits to retain after initial MASH screen step"
             help="These hits will be used to build a genome distance based tree for your experiment run. Default value of 2 is suitable for almost all scenarios."/>
         <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)" 
             help="This is the delimitor by which samples are grouped together to display in the final MultiQC report. For example, if your input data sets are mango_replicate1.fastq.gz, mango_replicate2.fastq.gz, orange_replicate1_maryland.fastq.gz, orange_replicate2_maryland.fastq.gz, then to create 2 samples mango and orange, the value for --fq_filename_delim would be _ (underscore) and the value for --fq_filename_delim_idx would be 1, since you want to group by the first word (i.e. mango or orange) after splitting the filename based on _ (underscore)."/>
@@ -152,7 +152,9 @@
         - Polished de novo assemblies (FASTA) for each sample.
         - Genome annotations (GFF) for each sample.
         - Whole genome distance based clustering tree (Newick).
-        - Additional metadata useful for uploading the Newick tree into iTOL. 
+        - Additional metadata useful for uploading the Newick tree into iTOL.
+        - A https://microreact.org URL stored in a TXT file. An attempt will be made to upload the tree (Newick)
+          to https://microreact.org and if successful, the URL will be retrieved and stored in this TXT file.
 
   ]]></help>
     <citations>