diff tree_relabeler.xml @ 0:02bc0d7d40b5 draft

planemo upload for repository https://github.com/phac-nml/galaxy_tools/blob/master/tools/tree_relabeler commit 974af0d5e7ccfcbd47284eb85a5f593d5e48daf8

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tree_relabeler.xml	Mon Apr 29 11:18:32 2019 -0400
@@ -0,0 +1,68 @@
+<tool id="tree_relabel" name="Tree Relabeler" version="1.0.0">
+    <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>
+
+    <inputs>
+        <param name="treefile" type="data" format="txt" 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."/>
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="output"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="treefile" value="phylogeneticTree.newick.nhx"/>
+	    <param name="tabfile" value="tabs.txt"/>
+	    <output name="output" file="results"/> 
+        </test>
+    </tests>
+    <help>
+
+What it does
+============
+
+This tool provides a means for relabeling the tips of a newick formatted tree.
+
+It takes a newick format tree file to modify tip labels and a tab-delimited file containing current tip labels and additional information to add to the tips in 2 or more columns. 
+
+Usage
+=====
+
+Header row of the tab delimited file must start with a '#'. An example is below:
+
+- #label outbreak    year    location
+- orgs1  outbreak1   year1   location1
+- orgs2  outbreak2   year2   location2
+
+and so on.
+
+The information in the tab file is inserted into the tree file so the new information will appear on the tip labels.
+
+
+Input
+=====
+
+Newick format tree
+
+Tab delimted file
+
+Desired delimiter for updated tip labels
+
+    </help>
+</tool>