--- a/cfsan_cronology.xml	Wed Nov 29 10:53:42 2023 -0500
+++ b/cfsan_cronology.xml	Mon Jul 15 16:11:44 2024 -0400
@@ -1,13 +1,12 @@
-<tool id="cfsan_cronology" name="cronology" version="0.1.0">
+<tool id="cfsan_cronology" name="cronology" version="0.2.0+galaxy23.1">
     <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="1.1.0">micromamba</requirement>
-        <requirement type="package">graphviz</requirement>
+        <container type="docker">quay.io/biocontainers/nextflow:24.04.3--hdfd78af_0</container>
     </requirements>    
     <version_command>nextflow -version</version_command>
     <command detect_errors="exit_code"><![CDATA[
 	mkdir -p cpipes-input || exit 1;
+    echo -e 'We attempted to create a tree and upload to microreact.org. The following is the log of that attempt\\nand contains the URL if it was successful.\\n\\n' > upload_to_microreact.txt || exit 1;
     pwd_path=\$(pwd);
     #import re
     #if (str($input_read_type_cond.input_read_type) == "single_long"):
@@ -49,9 +48,10 @@
     --tuspy_n $tuspy_n
 	--fq_filename_delim '${fq_filename_delim}'
 	--fq_filename_delim_idx $fq_filename_delim_idx
-	-profile kondagac;
-    mv './cpipes-output/cronology-multiqc/multiqc_report.html' './multiqc_report.html' > /dev/null 2>&1 || exit 1;
-    mv './cpipes-output/mashtree/hitsTree.dnd' './hitsTree.dnd' > /dev/null 2>&1 || exit 1;
+	-profile gxkubernetes;
+    mv './cpipes-output/cronology-multiqc/multiqc_report.html' './multiqc_report.html' || exit 1;
+    mv './cpipes-output/mashtree/hitsTree.dnd' './hitsTree.newick' > || exit 1;
+    cat ./cpipes-output/upload_microreact/microreact_url.txt >> upload_to_microreact.txt || exit 1;
     ]]></command>
     <inputs>
         <conditional name="input_read_type_cond">
@@ -83,7 +83,8 @@
     </inputs>
     <outputs>
         <data name="multiqc_report" format="html" label="cronology: MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/>
-        <data name="mashtree" format="newick" label="cronology: Genome distance based tree on ${on_string}" from_work_dir="hitsTree.dnd"/>
+        <data name="mashtree" format="nhx" label="cronology: Genome distance based tree on ${on_string}" from_work_dir="hitsTree.newick"/>
+        <data name="microreact" format="txt" label="cronology: Tree result from microreact.org ${on_string}" from_work_dir="upload_to_microreact.txt"/>
         <collection name="itol_metadata" type="list" label="cronology: iTOL Metadata: ${on_string}">
             <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" ext="txt" directory="./cpipes-output/cat_unique" match_relative_path="true" />
         </collection>