# HG changeset patch
# User nml
# Date 1561662193 14400
# Node ID 41ada87567a21adcb1e67e5469af7d74b5835828
# Parent  267858c28a34647564806bcb05a19267a0841db1
planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 8ad15943a8d365b3924ff7a5e53308cc56d7a6af

diff -r 267858c28a34 -r 41ada87567a2 test-data/replacedresults
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/replacedresults	Thu Jun 27 15:03:13 2019 -0400
@@ -0,0 +1,1 @@
+(newreference outbreak1 year1 location1:0.29121884);
\ No newline at end of file
diff -r 267858c28a34 -r 41ada87567a2 test-data/replacedtabs.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/replacedtabs.txt	Thu Jun 27 15:03:13 2019 -0400
@@ -0,0 +1,1 @@
+reference	newreference	outbreak1	year1	location1
diff -r 267858c28a34 -r 41ada87567a2 tree_relabeler.xml
--- a/tree_relabeler.xml	Thu Jun 20 12:45:02 2019 -0400
+++ b/tree_relabeler.xml	Thu Jun 27 15:03:13 2019 -0400
@@ -1,24 +1,20 @@
-<tool id="tree_relabel" name="Tree Relabeler" version="1.0.1">
+<tool id="tree_relabel" name="Tree Relabeler" version="1.1.0">
     <description>Relabels the tips of a newick formatted tree.</description>
 
     <requirements>
         <requirement type="package" version="1.7.2">perl-bioperl</requirement>
         <requirement type="package" version="2.49">perl-getopt-long</requirement>
     </requirements>
-
-    <stdio>
-        <exit_code range="1"  level="fatal"   description="Error opening a file."/>
-        <exit_code range="2"  level="fatal"   description="Error with tree format."/>
-    </stdio>
-
-    <command interpreter="perl">
-        nml_tree_relabeler.pl -i $treefile -t $tabfile -o $output -d $delim 
-    </command>
-
+  <command detect_errors="exit_code">
+    <![CDATA[
+             $__tool_directory__/nml_tree_relabeler.pl -i '$treefile' -t '$tabfile' -o '$output' -d '$delim' $replace
+    ]]>
+  </command>
     <inputs>
         <param name="treefile" type="data" format="nhx" label="The newick formated tree file to be relabeled:" optional="false"/>
         <param name="tabfile" type="data" format="txt" label="The tab separated file containing the current labels and the info to be added to the labels" optional="false"/>
         <param name="delim" type="text" label="Delimiter for new tip labels (space, _, etc)" optional="true" help="If left blank, labels of updated tips will be separated by spaces."/>
+        <param name="replace" truevalue='--replace' falsevalue='' type="boolean" label="Find and Replace current tip"  help="If false, will append to current tip. If true, will replace current tip"/>
     </inputs>
 
     <outputs>
@@ -31,6 +27,12 @@
 	    <param name="tabfile" value="tabs.txt"/>
 	    <output name="output" file="results"/> 
         </test>
+        <test>
+            <param name="treefile" value="phylogeneticTree.newick.nhx"/>
+	    <param name="tabfile" value="replacedtabs.txt"/>
+            <param name="replace" value="true"/>
+	    <output name="output" file="replacedresults"/>
+        </test>
     </tests>
     <help>
 
@@ -65,4 +67,6 @@
 Desired delimiter for updated tip labels
 
     </help>
+    <citations>
+    </citations>
 </tool>