# HG changeset patch
# User kkonganti
# Date 1701113427 18000
# Node ID 329a442629709c267da86ab06252e3c958f76816
# Parent  408603fd75ca562e28063be9dfd87b488f7ebe85
"planemo upload"

diff -r 408603fd75ca -r 329a44262970 cfsan_cronology.xml
--- a/cfsan_cronology.xml	Mon Nov 27 14:21:42 2023 -0500
+++ b/cfsan_cronology.xml	Mon Nov 27 14:30:27 2023 -0500
@@ -1,4 +1,4 @@
-<tool id="cfsan_cronology" name="cronology" version="0.1.0+galaxy0">
+<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>
@@ -74,7 +74,7 @@
         </conditional>
         <param name="refgenome" optional="true" value="GCF_003516125" type="text"
                 label="NCBI reference genome accession"
-                help="Is the reference genome other than <i>Cronobacter sakazakii</i>? Reference genome FASTA is used as a model for gene prediction. DO NOT ENTER THE DECIMAL PART (Ex: GCF_003516125.1)." />
+                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="10" 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)" 
@@ -85,13 +85,13 @@
         <data name="multiqc_report" format="html" label="cronology: MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/>
         <data name="mashtree" format="nwk" label="cronology: Genome distance based tree on ${on_string}" from_work_dir="hitsTree.dnd"/>
         <collection name="itol_metadata" type="list" label="cronology: iTOL Metadata: ${on_string}">
-            <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" ext="txt" match_relative_path="true" directory="./cpipes-output/cat_unique"/>
+            <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" ext="txt" directory="./cpipes-output/cat_unique" match_relative_path="true" />
         </collection>
         <collection name="gene_models" type="list" label="cronology: Predicted gene models: ${on_string}">
-            <discover_datasets pattern="(?P&lt;name&gt;.*)\.gff" ext="gff" match_relative_path="true" recurse="true" directory="./cpipes-output/prokka"/>
+            <discover_datasets pattern="(?P&lt;name&gt;.*)\.gff" ext="gff" directory="./cpipes-output/prokka" recurse="true" match_relative_path="true" />
         </collection>
         <collection name="assemblies" type="list" label="cronology: Polished genome assemblies: ${on_string}">
-            <discover_datasets pattern="(?P&lt;name&gt;.*)\.fa" ext="fa" match_relative_path="true" directory="./cpipes-output/polypolish"/>
+            <discover_datasets pattern="(?P&lt;name&gt;.*)\.fa" ext="fa" directory="./cpipes-output/polypolish" match_relative_path="true" />
         </collection>
     </outputs>
     <tests>