# HG changeset patch
# User kkonganti
# Date 1721075206 14400
# Node ID 1e6a6e88db167fff925b57c94b41f8633c214f78
# Parent  78a02e8cb092e66add1996f032c9f3983ce289de
planemo upload

diff -r 78a02e8cb092 -r 1e6a6e88db16 cfsan_cronology.xml
--- a/cfsan_cronology.xml	Mon Jul 15 16:16:59 2024 -0400
+++ b/cfsan_cronology.xml	Mon Jul 15 16:26:46 2024 -0400
@@ -6,7 +6,7 @@
     <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;
+    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($input_read_type_cond.input_read_type) == "single_long"):
@@ -34,7 +34,7 @@
 	        ln -sf '$pair.reverse' './cpipes-input/$read_R2';
 	    #end for
     #end if
-	$__tool_directory__/0.1.0/cpipes
+	$__tool_directory__/0.2.0/cpipes
     --pipeline cronology
     --input \${pwd_path}/cpipes-input
 	--output \${pwd_path}/cpipes-output
@@ -50,7 +50,7 @@
 	--fq_filename_delim_idx $fq_filename_delim_idx
 	-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;
+    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>