Mercurial > repos > earlhaminst > ete

diff ete_genetree_splitter.xml @ 9:b29ee6a16524 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 17c65045b726d0695814bfe761e534f6521786f1"
author earlhaminst
date Tue, 20 Oct 2020 15:10:40 +0000
parents f1eca1158f21
children 541a2ffc01ff
line wrap: on
line diff
--- a/ete_genetree_splitter.xml	Thu Oct 31 07:48:59 2019 -0400
+++ b/ete_genetree_splitter.xml	Tue Oct 20 15:10:40 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="ete_genetree_splitter" name="ETE GeneTree splitter" version="@VERSION@">
+<tool id="ete_genetree_splitter" name="ETE GeneTree splitter" version="@VERSION@+galaxy1">
     <description>from a genetree using the ETE Toolkit</description>
     <macros>
         <import>ete_macros.xml</import>
@@ -12,6 +12,7 @@
 python '$__tool_directory__/ete_genetree_splitter.py'
 --genetree '$genetreeFile'
 --gene_node $gene_node
+--split $splitter
 #if $gainlose_conditional.gainlose == "True"
     --speciestree '$gainlose_conditional.speciesFile'
     --species_format $gainlose_conditional.species_format
@@ -25,6 +26,10 @@
             <option value="0" selected="true">gene_species</option>
             <option value="1">species_gene</option>
         </param>
+        <param name="splitter" type="select" label="GeneTree splitting algorithm">
+            <option value="dups">Split by Duplication</option>
+            <option value="treeko">Split using TreeKO algorithm</option>
+        </param>
         <conditional name="gainlose_conditional">
             <param name="gainlose" type="select" label="Find out gene gain/lose">
                 <option value="True">Yes</option>
@@ -72,6 +77,7 @@
         <test>
             <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
             <param name="gene_node" value="0"/>
+            <param name="splitter" value="dups"/>
             <param name="output_format" value="9" />
             <output_collection name="genetrees_lists" type="list" count="4">
                 <element name="1" file="11_genetree.nhx" ftype="nhx" />
@@ -83,6 +89,7 @@
         <test>
             <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
             <param name="gene_node" value="0"/>
+            <param name="splitter" value="dups"/>
             <param name="gainlose" value="True" />
             <param name="speciesFile" ftype="nhx" value="speciestree.nhx" />
             <param name="species_format" value="8" />
@@ -95,6 +102,18 @@
                 <element name="5" file="25_genetree.nhx" ftype="nhx" />
             </output_collection>
         </test>
+        <test>
+            <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
+            <param name="gene_node" value="0"/>
+            <param name="splitter" value="treeko"/>
+            <param name="output_format" value="9" />
+            <output_collection name="genetrees_lists" type="list" count="5">
+                <element name="1" file="31_genetree.nhx" ftype="nhx" />
+                <element name="2" file="32_genetree.nhx" ftype="nhx" />
+                <element name="3" file="33_genetree.nhx" ftype="nhx" />
+                <element name="4" file="34_genetree.nhx" ftype="nhx" />
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[
 Split GeneTrees from single GeneTree by duplication event using the `ETE Toolkit`_.