# HG changeset patch
# User rnateam
# Date 1488214958 18000
# Node ID 606440a3852d2bf3715144923bf88c730588766c
# Parent  5970f6f2a36b7c79f6553bc7958cb327ae10be4e
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 5a545fc913b3a07e1452e67f66b2ca593660abdf

diff -r 5970f6f2a36b -r 606440a3852d locarna_best_subtree.xml
--- a/locarna_best_subtree.xml	Wed Feb 22 16:51:35 2017 -0500
+++ b/locarna_best_subtree.xml	Mon Feb 27 12:02:38 2017 -0500
@@ -1,6 +1,6 @@
-<tool id="locarna_best_subtree" name="locarna_best_subtree" version="0.1.0" >
+<tool id="locarna_best_subtree" name="locarna_graphclust" version="0.1.0" >
   <requirements>
-    <requirement type="package" version="0.1.8">graphclust-wrappers</requirement>
+    <requirement type="package" version="0.1.9">graphclust-wrappers</requirement>
     <requirement type="package" version='1.8.10'>locarna</requirement>
     <requirement type="package" version='2.1'>rnaz</requirement>
     <requirement type="package" version='0.07'>perl-math-round</requirement>
@@ -11,7 +11,7 @@
   <command>
     <![CDATA[
 
-        'locARNAGraphClust.pl'  '$center_fa_file' '$tree_file' '$tree_matrix' '$data_map'
+        'locARNAGraphClust.pl'  '$center_fa_file' '$tree_file' '$tree_matrix' '$data_map' $allow_overlap
         #if str($param_type.param_type_selector) == "gclust"
              $param_type.p
             $param_type.max_diff_am
@@ -32,7 +32,7 @@
     <param type="data" name="tree_file" label="trees" format="text" help="text format" />
     <param type="data" name="tree_matrix" label="tree_matrix" format="text" help="text format" />
     <param type="data" name="data_map" label="data_map" format="txt" help="text format" />
-
+    <param name="allow_overlap" type="boolean"  truevalue="1" falsevalue="0" label="Allow overlap in subtrees" help="otherwise ignore subtree if it contains overlapping sequences"/>
 
     <conditional name="param_type">
     <param name="param_type_selector" type="select" label="Choose the type of parameters">
@@ -77,7 +77,6 @@
 
   </inputs>
   <outputs>
-
     <data name="model_tree_stk" format="stockholm" label="model.tree.stk" from_work_dir="MODEL/best_subtree.aln" />
   </outputs>
   <tests>
@@ -86,6 +85,7 @@
       <param name="center_fa_file" value="1.1.center.fa"/>
       <param name="data_map" value="data.map"/>
       <param name="tree_matrix" value="1.1.matrix.tree"/>
+      <param name="allow_overlap" value="0"/>
       <conditional name="param_type">
         <param name="iteration_num_selector" value="gclust"/>
         <param name="p" value="0.001"/>