# HG changeset patch
# User kkonganti
# Date 1701112696 18000
# Node ID c6327baca625e9dd8fe330f9ecf7207b5dfcb01f
# Parent  c8597e9e1a97c11da5d5d5a99f35a574afa52688
"planemo upload"

diff -r c8597e9e1a97 -r c6327baca625 cfsan_cronology.xml
--- a/cfsan_cronology.xml	Mon Nov 27 12:37:44 2023 -0500
+++ b/cfsan_cronology.xml	Mon Nov 27 14:18:16 2023 -0500
@@ -1,9 +1,9 @@
 <tool id="cfsan_cronology" name="cronology" version="0.1.0">
     <description>An automated workflow for Cronobacter isolate assembly, sequence typing and traceback.</description>
     <requirements>
-	<requirement type="package" version="23.04">nextflow</requirement>
-    <requirement type="package" version="1.0.0">micromamba</requirement>
-	<requirement type="package">graphviz</requirement>
+        <requirement type="package" version="23.04">nextflow</requirement>
+        <requirement type="package" version="1.0.0">micromamba</requirement>
+        <requirement type="package">graphviz</requirement>
     </requirements>    
     <version_command>nextflow -version</version_command>
     <command detect_errors="exit_code"><![CDATA[
@@ -131,10 +131,8 @@
 **Testing and Validation**
 
 The CPIPES - cronology Nextflow pipeline has been wrapped to make it work in Galaxy. It takes in either paired or unpaired short reads list as an input 
-and generates a MultiQC report in the final step. The pipeline has been tested on 2x300 bp MiSeq and 2x150 bp NextSeq simulated reads and has been shown to call multiple
-Salmonella serotypes with up to ~95% accuracy. The pipeline has also been tested on metagenomics data sets from Peach and Papaya outbreaks as discussed in 
-our publication (https://www.frontiersin.org/articles/10.3389/fmicb.2023.1200983/full). All the original testing and validation was 
-done on the command line on the CFSAN Raven2 HPC Cluster.
+and performs read quality control followed by de novo assembly, gene prediction and annotation, sequence typing and whole genome distance based clustering.
+All the testing has been done on the command line on the CFSAN Raven2 HPC Cluster.
 
 
 ----
@@ -143,7 +141,7 @@
 
 **Outputs**
 
-The main output file is a:
+The main output files are:
 
     ::
 
@@ -152,6 +150,10 @@
                           work within Galaxy for the MultiQC report. Please download the file by clicking
                           on the floppy icon and view it in your browser on your local desktop/workstation.
                           You can export the tables and plots from the downloaded MultiQC report.
+        - 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. 
 
   ]]></help>
     <citations>
@@ -160,10 +162,10 @@
             author = {Konganti, Kranti},
             year = {2023},
             month = {August},
-            title = {cronology: better calling of Salmonella serotypes from enrichment cultures using shotgun metagenomic profiling and its application in an outbreak setting},
-            journal = {Frontiers in Microbiology},
-            doi = {10.3389/fmicb.2023.1200983},
-            url = {https://www.frontiersin.org/articles/10.3389/fmicb.2023.1200983/full}}
+            title = {cronology: An automated workflow for Cronobacter isolate assembly, sequence typing and traceback},
+            journal = {Unpublished},
+            doi = {10.3389/fmicb.2023.120098312},
+            url = {https://github.com/CFSAN-Biostatistics/cronology}}
         </citation>
     </citations>
 </tool>