# HG changeset patch
# User earlhaminst
# Date 1741649297 0
# Node ID e4d5d9a69c9d2cc4bcdc8435117af703186092e1
# Parent  1e85af7a29c48903532fb016098482c49e589773
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit a0d7ab86b86bb764e457767bf8e8bc29868d0cbb

diff -r 1e85af7a29c4 -r e4d5d9a69c9d ete_gene_cnv.xml
--- a/ete_gene_cnv.xml	Mon Feb 24 16:34:12 2025 +0000
+++ b/ete_gene_cnv.xml	Mon Mar 10 23:28:17 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="ete_gene_csv_finder" name="Gene Copy Number Finder" version="@VERSION@">
+<tool id="ete_gene_csv_finder" name="Gene Copy Number Finder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>from a genetree using the ETE Toolkit</description>
     <macros>
         <import>ete_macros.xml</import>
diff -r 1e85af7a29c4 -r e4d5d9a69c9d ete_genetree_splitter.xml
--- a/ete_genetree_splitter.xml	Mon Feb 24 16:34:12 2025 +0000
+++ b/ete_genetree_splitter.xml	Mon Mar 10 23:28:17 2025 +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="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>from a genetree using the ETE Toolkit</description>
     <macros>
         <import>ete_macros.xml</import>
@@ -91,7 +91,9 @@
         <test>
             <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
             <param name="gene_node" value="0"/>
-            <param name="splitter" value="dups"/>
+            <conditional name="splitting_conditional">
+                <param name="splitter" value="dups"/>
+            </conditional>
             <param name="output_format" value="9" />
             <output_collection name="genetrees_lists" type="list" count="4">
                 <element name="1" file="11_genetree.nhx" ftype="nhx" />
@@ -103,10 +105,14 @@
         <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" />
+            <conditional name="splitting_conditional">
+                <param name="splitter" value="dups"/>
+            </conditional>
+            <conditional name="gainlose_conditional">
+                <param name="gainlose" value="True" />
+                <param name="speciesFile" ftype="nhx" value="speciestree.nhx" />
+                <param name="species_format" value="8" />
+            </conditional>
             <param name="output_format" value="9" />
             <output_collection name="genetrees_lists" type="list" count="5">
                 <element name="1" file="21_genetree.nhx" ftype="nhx" />
@@ -119,7 +125,9 @@
         <test>
             <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
             <param name="gene_node" value="0"/>
-            <param name="splitter" value="treeko"/>
+            <conditional name="splitting_conditional">
+                <param name="splitter" value="treeko"/>
+            </conditional>
             <param name="output_format" value="9" />
             <output_collection name="genetrees_lists" type="list" count="4">
                 <element name="1" file="31_genetree.nhx" ftype="nhx" />
@@ -132,9 +140,11 @@
         <test>
             <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
             <param name="gene_node" value="0"/>
-            <param name="splitter" value="species"/>
-            <param name="ingroup" value="pantroglodytes,homosapiens,rattusnorvegicus,musmusculus,canisfamiliaris" />
-            <param name="outgroup" value="susscrofa" />
+            <conditional name="splitting_conditional">
+                <param name="splitter" value="species"/>
+                <param name="ingroup" value="pantroglodytes,homosapiens,rattusnorvegicus,musmusculus,canisfamiliaris" />
+                <param name="outgroup" value="susscrofa" />
+            </conditional>
             <param name="output_format" value="9" />
             <output_collection name="genetrees_lists" type="list" count="4">
                 <element name="1" file="41_genetree.nhx" ftype="nhx" />
diff -r 1e85af7a29c4 -r e4d5d9a69c9d ete_homology_classifier.xml
--- a/ete_homology_classifier.xml	Mon Feb 24 16:34:12 2025 +0000
+++ b/ete_homology_classifier.xml	Mon Mar 10 23:28:17 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="ete_homology_classifier" name="Homology Classifier and Filter" version="@VERSION@">
+<tool id="ete_homology_classifier" name="Homology Classifier and Filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>from a genetree using the ETE Toolkit</description>
     <macros>
         <import>ete_macros.xml</import>
@@ -50,13 +50,17 @@
     <tests>
         <test>
             <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
-            <param name="out_format" value="tabular"/>
-            <param name="homologies" value="one-to-one,one-to-many,many-to-one,many-to-many,paralogs" />
+            <conditional name="format_type">
+                <param name="out_format" value="tabular"/>
+                <param name="homologies" value="one-to-one,one-to-many,many-to-one,many-to-many,paralogs" />
+            </conditional>
             <output name="homology" file="11_homology.tabular" />
         </test>
         <test>
             <param name="genetreeFile" ftype="nhx" value="11_genetree.nhx" />
-            <param name="out_format" value="csv"/>
+            <conditional name="format_type">
+                <param name="out_format" value="csv"/>
+            </conditional>
             <output name="homology" file="11_homology.csv" />
         </test>
     </tests>
diff -r 1e85af7a29c4 -r e4d5d9a69c9d ete_init_taxdb.xml
--- a/ete_init_taxdb.xml	Mon Feb 24 16:34:12 2025 +0000
+++ b/ete_init_taxdb.xml	Mon Mar 10 23:28:17 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="ete_init_taxdb" name="ETE taxa DB generator" version="@VERSION@">
+<tool id="ete_init_taxdb" name="ETE taxa DB generator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>generates the ETE sqlite DB from the NCBI taxdump.tar.gz</description>
     <macros>
         <import>ete_macros.xml</import>
@@ -29,8 +29,10 @@
     </outputs>
     <tests>
         <test>
-            <param name="latest" value="local" />
-            <param name="taxdump" ftype="tar" value="taxdump.tar.gz" />
+            <conditional name="latestcond">
+                <param name="latest" value="local" />
+                <param name="taxdump" ftype="tar" value="taxdump.tar.gz" />
+            </conditional>
             <output name="database" file="taxdump.sqlite" compare="sim_size" />
         </test>
     </tests>
diff -r 1e85af7a29c4 -r e4d5d9a69c9d ete_lineage_generator.xml
--- a/ete_lineage_generator.xml	Mon Feb 24 16:34:12 2025 +0000
+++ b/ete_lineage_generator.xml	Mon Mar 10 23:28:17 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="ete_lineage_generator" name="ETE lineage generator" version="@VERSION@">
+<tool id="ete_lineage_generator" name="ETE lineage generator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>from a list of species/taxids using the ETE Toolkit</description>
     <macros>
         <import>ete_macros.xml</import>
@@ -88,37 +88,53 @@
         <test>
             <param name="speciesFile" ftype="txt" value="species.txt" />
             <param name="database" ftype="sqlite" value="taxdump.sqlite" />
-            <param name="compress" value="" />
-            <param name="levels" value="full" />
+            <conditional name="compresscond">
+                <param name="compress" value="" />
+            </conditional>
+            <conditional name="ranks">
+                <param name="levels" value="full" />
+            </conditional>
             <output name="outputFile" file="lineage.txt" />
         </test>
         <test>
             <param name="speciesFile" ftype="txt" value="species.txt" />
             <param name="database" ftype="sqlite" value="taxdump.sqlite" />
-            <param name="compress" value="-c" />
-            <param name="levels" value="primary" />
+            <conditional name="compresscond">
+                <param name="compress" value="-c" />
+            </conditional>
+            <conditional name="ranks">
+                <param name="levels" value="primary" />
+            </conditional>
             <output name="outputFile" file="lineage-compress.txt" />
         </test>
         <test>
             <param name="speciesFile" ftype="txt" value="species.txt" />
             <param name="database" ftype="sqlite" value="taxdump.sqlite" />
-            <param name="compress" value="-c" />
-            <param name="levels" value="primary" />
-            <param name="lower" value="-l" />
+            <conditional name="compresscond">
+                <param name="compress" value="-c" />
+                <param name="lower" value="true" />
+            </conditional>
+            <conditional name="ranks">
+                <param name="levels" value="primary" />
+            </conditional>
             <output name="outputFile" file="lineage-compress-lower.txt" />
         </test>
         <test>
             <param name="speciesFile" ftype="txt" value="species.txt" />
             <param name="database" ftype="sqlite" value="taxdump.sqlite" />
-            <param name="compress" value="" />
-            <param name="levels" value="manual" />
-            <param name="manualranks" value="kingdom,family" />
+            <conditional name="compresscond">
+                <param name="compress" value="" />
+            </conditional>
+            <conditional name="ranks">
+                <param name="levels" value="manual" />
+                <param name="manualranks" value="kingdom,family" />
+            </conditional>
             <output name="outputFile" file="lineage-full.txt" />
         </test>
         <test>
             <param name="speciesFile" ftype="txt" value="species.txt" />
             <param name="database" ftype="sqlite" value="taxdump.sqlite" />
-            <param name="includeid" value="--includeid" />
+            <param name="includeid" value="true" />
             <output name="outputFile" file="lineage-wid.txt" />
         </test>
         <test>
diff -r 1e85af7a29c4 -r e4d5d9a69c9d ete_macros.xml
--- a/ete_macros.xml	Mon Feb 24 16:34:12 2025 +0000
+++ b/ete_macros.xml	Mon Mar 10 23:28:17 2025 +0000
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@VERSION@">3.1.3</token>
+    <token name="@TOOL_VERSION@">3.1.3</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="bio_tools">
         <xrefs>
             <xref type="bio.tools">ete</xref>
@@ -8,7 +9,9 @@
     </xml>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">ete3</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">ete3</requirement>
+            <!-- Workaround for https://github.com/etetoolkit/ete/pull/770 until ete3 >3.1.3 is released -->
+            <requirement type="package" version="3.40">sqlite</requirement>
         </requirements>
     </xml>
     <xml name="citations">
diff -r 1e85af7a29c4 -r e4d5d9a69c9d ete_mod.xml
--- a/ete_mod.xml	Mon Feb 24 16:34:12 2025 +0000
+++ b/ete_mod.xml	Mon Mar 10 23:28:17 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="ete3_mod" name="ETE mod" version="@VERSION@">
+<tool id="ete3_mod" name="ETE mod" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>manipulates tree topology by rooting, pruning or sorting branches</description>
     <macros>
         <import>ete_macros.xml</import>
@@ -73,32 +73,32 @@
         <test>
             <param name="input_trees" ftype="nhx" value="tree1.nhx" />
             <param name="prune" value="A,C" />
-            <param name="prune_preserve_lengths" value="--prune_preserve_lengths" />
+            <param name="prune_preserve_lengths" value="true" />
             <output name="output_tree" file="tree1_pruneACpreserve.nhx" />
         </test>
         <test>
             <param name="input_trees" ftype="nhx" value="tree1.nhx" />
-            <param name="unroot" value="--unroot" />
+            <param name="unroot" value="true" />
             <output name="output_tree" file="tree1_unroot.nhx" />
         </test>
         <test>
             <param name="input_trees" ftype="nhx" value="tree2.nhx" />
-            <param name="sort_branches" value="--sort_branches" />
+            <param name="sort_branches" value="true" />
             <output name="output_tree" file="tree2_sort.nhx" />
         </test>
         <test>
             <param name="input_trees" ftype="nhx" value="tree1.nhx" />
-            <param name="ladderize" value="--ladderize" />
+            <param name="ladderize" value="true" />
             <output name="output_tree" file="tree1_ladder.nhx" />
         </test>
         <test>
             <param name="input_trees" ftype="nhx" value="tree1_unroot.nhx" />
-            <param name="resolve_polytomies" value="--resolve_polytomies" />
+            <param name="resolve_polytomies" value="true" />
             <output name="output_tree" file="tree1_unroot_resolve.nhx" />
         </test>
         <test>
             <param name="input_trees" ftype="nhx" value="tree3.nhx" />
-            <param name="standardize" value="--standardize" />
+            <param name="standardize" value="true" />
             <output name="output_tree" file="tree3_stand.nhx" />
         </test>
     </tests>
diff -r 1e85af7a29c4 -r e4d5d9a69c9d ete_species_tree_generator.py
--- a/ete_species_tree_generator.py	Mon Feb 24 16:34:12 2025 +0000
+++ b/ete_species_tree_generator.py	Mon Mar 10 23:28:17 2025 +0000
@@ -22,7 +22,6 @@
 with open(options.input_species_filename) as f:
     species_name = [_.strip().replace('_', ' ') for _ in f.readlines()]
 
-breakpoint()
 name2taxid = ncbi.get_name_translator(species_name)
 
 taxid = [name2taxid[_][0] for _ in species_name]
diff -r 1e85af7a29c4 -r e4d5d9a69c9d ete_species_tree_generator.xml
--- a/ete_species_tree_generator.xml	Mon Feb 24 16:34:12 2025 +0000
+++ b/ete_species_tree_generator.xml	Mon Mar 10 23:28:17 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="ete_species_tree_generator" name="ETE species tree generator" version="@VERSION@">
+<tool id="ete_species_tree_generator" name="ETE species tree generator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>from a list of species using the ETE Toolkit</description>
     <macros>
         <import>ete_macros.xml</import>
@@ -54,7 +54,9 @@
         <test>
             <param name="speciesFile" ftype="txt" value="species.txt" />
             <param name="database" ftype="sqlite" value="taxdump.sqlite" />
-            <param name="treebest" value="yes" />
+            <conditional name="output_format">
+                <param name="treebest" value="yes" />
+            </conditional>
             <output name="outputFile">
                 <assert_contents>
                     <has_text text="(Homosapiens*,Pantroglodytes*,Gorillagorillagorilla*)" />