# HG changeset patch
# User earlhaminst
# Date 1603206640 0
# Node ID b29ee6a16524a4630e0d2a355dd5950a85095d63
# Parent  16e925bf567e78dd9d7bddffd255af68063f2d5f
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 17c65045b726d0695814bfe761e534f6521786f1"

diff -r 16e925bf567e -r b29ee6a16524 ete_genetree_splitter.py
--- a/ete_genetree_splitter.py	Thu Oct 31 07:48:59 2019 -0400
+++ b/ete_genetree_splitter.py	Tue Oct 20 15:10:40 2020 +0000
@@ -13,6 +13,7 @@
     parser.add_option('--species_format', type='int', default=8, help='Species Tree input format (0-9)')
     parser.add_option('--gene_node', type='int', default=0, help='Gene node format 0=gene_species, 1=species_gene')
     parser.add_option('--gainlose', action='store_true', default=False, help='Find out gene gain/lose')
+    parser.add_option('--split', type='choice', choices=['dups', 'treeko'], dest="split", default='dups', help='Choose GeneTree splitting algorithms')
     parser.add_option('--output_format', type='int', default=9, help='GeneTree output format (0-9)')
     options, args = parser.parse_args()
 
@@ -47,11 +48,22 @@
 
         genetree, events = genetree.reconcile(speciestree)
 
-    # splits tree by duplication events which returns the list of all subtrees resulting from splitting current tree by its duplication nodes.
-    for cluster_id, node in enumerate(genetree.split_by_dups(), 1):
-        outfile = str(cluster_id) + '_genetree.nhx'
-        with open(outfile, 'w') as f:
-            f.write(node.write(format=options.output_format))
+    if options.split == "dups":
+        # splits tree by duplication events which returns the list of all subtrees resulting from splitting current tree by its duplication nodes.
+        for cluster_id, node in enumerate(genetree.split_by_dups(), 1):
+            outfile = str(cluster_id) + '_genetree.nhx'
+            with open(outfile, 'w') as f:
+                f.write(node.write(format=options.output_format))
+    elif options.split == "treeko":
+        # splits tree using the TreeKO algorithm.
+        ntrees, ndups, sptrees = genetree.get_speciation_trees()
+
+        cluster_id = 0
+        for spt in sptrees:
+            cluster_id = cluster_id + 1
+            outfile = str(cluster_id) + '_genetree.nhx'
+            with open(outfile, 'w') as f:
+                f.write(spt.write(format=options.output_format))
 
 
 def parse_sp_name(node_name):
diff -r 16e925bf567e -r b29ee6a16524 ete_genetree_splitter.xml
--- 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`_.
diff -r 16e925bf567e -r b29ee6a16524 ete_lineage_generator.py
--- a/ete_lineage_generator.py	Thu Oct 31 07:48:59 2019 -0400
+++ b/ete_lineage_generator.py	Tue Oct 20 15:10:40 2020 +0000
@@ -41,17 +41,19 @@
     RANK_IDX: mapping from rank names to indices (distance to root/leaf?)
     lower: use lower taxa for filling "NA"s
     """
-    lineage = ncbi.get_lineage(taxid)
-    lineage_ranks = ncbi.get_rank(lineage)
-    lineage_names = ncbi.get_taxid_translator(lineage, try_synonyms=True)
+    lineage_taxids = ncbi.get_lineage(taxid)
+    lineage_ranks = ncbi.get_rank(lineage_taxids)
+    lineage_names = ncbi.get_taxid_translator(lineage_taxids, try_synonyms=True)
     if lower:
-        lineage.reverse()
-    for l in lineage:
-        if not lineage_ranks[l] in RANK_IDX:
+        lineage_taxids.reverse()
+    for parent_taxid in lineage_taxids:
+        parent_rank = lineage_ranks[parent_taxid]
+        if parent_rank not in RANK_IDX:
             continue
-        if ranks[RANK_IDX[lineage_ranks[l]]] != "NA":
+        parent_rank_index = RANK_IDX[parent_rank]
+        if ranks[parent_rank_index] != "NA":
             continue
-        ranks[RANK_IDX[lineage_ranks[l]]] = lineage_names[l]
+        ranks[parent_rank_index] = lineage_names[parent_taxid]
 
 
 # get command line options
diff -r 16e925bf567e -r b29ee6a16524 test-data/31_genetree.nhx
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/31_genetree.nhx	Tue Oct 20 15:10:40 2020 +0000
@@ -0,0 +1,1 @@
+(((insr_rattusnorvegicus,insr_musmusculus),(insr_homosapiens,insr_pantroglodytes)),insr_susscrofa);
\ No newline at end of file
diff -r 16e925bf567e -r b29ee6a16524 test-data/32_genetree.nhx
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/32_genetree.nhx	Tue Oct 20 15:10:40 2020 +0000
@@ -0,0 +1,1 @@
+((maob_rattusnorvegicus,maob_musmusculus),((maob_homosapiens,maob_pantroglodytes),(maob_susscrofa,maob_canisfamiliaris)));
\ No newline at end of file
diff -r 16e925bf567e -r b29ee6a16524 test-data/33_genetree.nhx
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/33_genetree.nhx	Tue Oct 20 15:10:40 2020 +0000
@@ -0,0 +1,1 @@
+(((maoa_rattusnorvegicus,maoa_musmusculus),(maoa_homosapiens,maoa_pantroglodytes)),(maoa_susscrofa,maoa_canisfamiliaris));
\ No newline at end of file
diff -r 16e925bf567e -r b29ee6a16524 test-data/34_genetree.nhx
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/34_genetree.nhx	Tue Oct 20 15:10:40 2020 +0000
@@ -0,0 +1,1 @@
+(((brat1_rattusnorvegicus,brat1_musmusculus),(brat1_homosapiens,brat1_pantroglodytes)),(brat1_susscrofa,brat1_canisfamiliaris));
\ No newline at end of file