# HG changeset patch
# User abims-sbr
# Date 1521191382 14400
# Node ID ad3446d7f79416e9fd5f1c283436fc348d52006c
# Parent  59f4b9ffd92b0ce3a7d02514ea8d3cbef41a1054
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 10673955482e3c7641d9c2228265b6b69fcba4b8

diff -r 59f4b9ffd92b -r ad3446d7f794 ConcatPhyl.xml
--- a/ConcatPhyl.xml	Wed Feb 28 10:39:19 2018 -0500
+++ b/ConcatPhyl.xml	Fri Mar 16 05:09:42 2018 -0400
@@ -199,11 +199,11 @@
 			<filter>format['format_run'] == "nucleic" and out == "nexus"</filter>
 		</data>
 
-		<data name="out_raxml1" format="txt" label="Phylogeny_RAxML_BestTree" from_work_dir="RAxML_bestTree.galaxy_run">
+		<data name="out_raxml1" format="nhx" label="Phylogeny_RAxML_BestTree" from_work_dir="RAxML_bestTree.galaxy_run">
 			<filter>raxml1 == True</filter>
 		</data>
 
-		<data name="out_raxml3" format="txt" label="Phylogeny_RAxML_BiPartition" from_work_dir="RAxML_bipartitions.galaxy_run">
+		<data name="out_raxml3" format="nhx" label="Phylogeny_RAxML_BiPartition" from_work_dir="RAxML_bipartitions.galaxy_run">
 			<filter>raxml3 == True</filter>
 		</data>
 
@@ -255,8 +255,8 @@
             <param name="raxml1" value="True" />
             <param name="raxml3" value="True" />
             <param name="raxml4" value="True" />
-            <output name="out_raxml1" value="RAxML_bestTree"/>     
-            <output name="out_raxml3" value="RAxML_bipartitions"/>                
+            <output name="out_raxml1" value="RAxML_bestTree.nwk"/>     
+            <output name="out_raxml3" value="RAxML_bipartitions.nwk"/>                
         </test>
         
         <test>
@@ -275,8 +275,8 @@
             <param name="raxml1" value="True" />
             <param name="raxml3" value="True" />
             <param name="raxml4" value="True" />
-            <output name="out_raxml1" value="RAxML_bestTree_test3"/>     
-            <output name="out_raxml3" value="RAxML_bipartitions_test3"/>                
+            <output name="out_raxml1" value="RAxML_bestTree_test3.nwk"/>     
+            <output name="out_raxml3" value="RAxML_bipartitions_test3.nwk"/>                
         </test>
 	</tests>
 
diff -r 59f4b9ffd92b -r ad3446d7f794 test-data/RAxML_bestTree
--- a/test-data/RAxML_bestTree	Wed Feb 28 10:39:19 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-((Th:0.14924410568595378179,(Pg:0.09556296125671981390,Am:0.18536781449475758787):0.03651339268974715391):0.09478352424348672478,(Ap:0.01138298824199455994,Ph:0.14438335285430420329):0.01626011361346790460,Ac:0.01818704284736943205):0.0;
diff -r 59f4b9ffd92b -r ad3446d7f794 test-data/RAxML_bestTree.nwk
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RAxML_bestTree.nwk	Fri Mar 16 05:09:42 2018 -0400
@@ -0,0 +1,1 @@
+((Th:0.14924410568595378179,(Pg:0.09556296125671981390,Am:0.18536781449475758787):0.03651339268974715391):0.09478352424348672478,(Ap:0.01138298824199455994,Ph:0.14438335285430420329):0.01626011361346790460,Ac:0.01818704284736943205):0.0;
diff -r 59f4b9ffd92b -r ad3446d7f794 test-data/RAxML_bestTree_test3
--- a/test-data/RAxML_bestTree_test3	Wed Feb 28 10:39:19 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-((Th:0.14927144427385935499,(Am:0.18539294342267700899,Pg:0.09554925527172976329):0.03654579746795907913):0.09478496426471696990,(Ap:0.01138646621287440173,Ph:0.14439022038764615097):0.01625809813917244995,Ac:0.01818713970915995445):0.0;
diff -r 59f4b9ffd92b -r ad3446d7f794 test-data/RAxML_bestTree_test3.nwk
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RAxML_bestTree_test3.nwk	Fri Mar 16 05:09:42 2018 -0400
@@ -0,0 +1,1 @@
+((Th:0.14927144427385935499,(Am:0.18539294342267700899,Pg:0.09554925527172976329):0.03654579746795907913):0.09478496426471696990,(Ap:0.01138646621287440173,Ph:0.14439022038764615097):0.01625809813917244995,Ac:0.01818713970915995445):0.0;
diff -r 59f4b9ffd92b -r ad3446d7f794 test-data/RAxML_bipartitions
--- a/test-data/RAxML_bipartitions	Wed Feb 28 10:39:19 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-(Ph:0.14438335285430420329,(Ac:0.01818704284736943205,(Th:0.14924410568595378179,(Pg:0.09556296125671981390,Am:0.18536781449475758787)75:0.03651339268974715391)98:0.09478352424348672478)86:0.01626011361346790460,Ap:0.01138298824199455994);
diff -r 59f4b9ffd92b -r ad3446d7f794 test-data/RAxML_bipartitions.nwk
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RAxML_bipartitions.nwk	Fri Mar 16 05:09:42 2018 -0400
@@ -0,0 +1,1 @@
+(Ph:0.14438335285430420329,(Ac:0.01818704284736943205,(Th:0.14924410568595378179,(Pg:0.09556296125671981390,Am:0.18536781449475758787)75:0.03651339268974715391)98:0.09478352424348672478)86:0.01626011361346790460,Ap:0.01138298824199455994);
diff -r 59f4b9ffd92b -r ad3446d7f794 test-data/RAxML_bipartitions_test3
--- a/test-data/RAxML_bipartitions_test3	Wed Feb 28 10:39:19 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-(Ph:0.14439022038764615097,(Ac:0.01818713970915995445,(Th:0.14927144427385935499,(Am:0.18539294342267700899,Pg:0.09554925527172976329)78:0.03654579746795907913)99:0.09478496426471696990)86:0.01625809813917244995,Ap:0.01138646621287440173);
diff -r 59f4b9ffd92b -r ad3446d7f794 test-data/RAxML_bipartitions_test3.nwk
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RAxML_bipartitions_test3.nwk	Fri Mar 16 05:09:42 2018 -0400
@@ -0,0 +1,1 @@
+(Ph:0.14439022038764615097,(Ac:0.01818713970915995445,(Th:0.14927144427385935499,(Am:0.18539294342267700899,Pg:0.09554925527172976329)78:0.03654579746795907913)99:0.09478496426471696990)86:0.01625809813917244995,Ap:0.01138646621287440173);