# HG changeset patch
# User rnateam
# Date 1485038376 18000
# Node ID c6c4a7adb099aeeb92fc2cca8bacfb82b785b33a
# Parent  15bd4fb05e5c73dcd6e522602cece70d6046ae93
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/LocARNAGraphClust commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86

diff -r 15bd4fb05e5c -r c6c4a7adb099 locarna_best_subtree.xml
--- a/locarna_best_subtree.xml	Fri Dec 16 07:35:29 2016 -0500
+++ b/locarna_best_subtree.xml	Sat Jan 21 17:39:36 2017 -0500
@@ -1,49 +1,110 @@
 <tool id="locarna_best_subtree" name="locarna_best_subtree" version="0.1.0" >
-	<requirements>
-		<requirement type="package" version="0.1">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>
-	</requirements>
-	<stdio>
-		<exit_code range="1:" />
-	</stdio>
-	<command>
-		<![CDATA[
+  <requirements>
+    <requirement type="package" version="0.1.7">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>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+  <command>
+    <![CDATA[
 
-		    'locARNAGraphClust.pl'  '$center_fa_file' '$tree_file' '$tree_matrix' $p $max_diff_am $tau $max_diff '' '$data_map' $plfold_minlen
+        'locARNAGraphClust.pl'  '$center_fa_file' '$tree_file' '$tree_matrix' '$data_map'
+        #if str($param_type.param_type_selector) == "gclust"
+             $param_type.p
+            $param_type.max_diff_am
+            $param_type.max_diff
+            $param_type.tau
+            $param_type.plfold_minlen
+            $param_type.struct_weight
+            $param_type.indel_opening
+            $param_type.indel
+            $param_type.alifold_consensus_dp
+            $param_type.plfold_span
+            $param_type.plfold_winsize
+         #end if
         ]]>
-	</command>
-	<inputs>
-		<param type="data" name="center_fa_file" label="centers" format="fa, fasta" help="fasta format" />
-		<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="p" type="float" value="0.001" size="5" label="minimal probability" help="-p"/>
-		<param name="max_diff_am" type="integer" value="50" size="5" label=" maximal difference for sizes of matched arcs" help="--max-diff-am"/>
-		<param name="tau" type="integer" value="50" size="5" label="Tau factor in percent" help="--tau"/>
-		<param name="max_diff" type="integer" value="100" size="5" label="maximal difference for alignment traces" help="--max-diff"/>
-		<param name="plfold_minlen" type="integer" value="210" size="5" label="Minimal length of a sequences for which RNAplfold is used" />
-	</inputs>
-	<outputs>
+  </command>
+  <inputs>
+    <param type="data" name="center_fa_file" label="centers" format="fa, fasta" help="fasta format" />
+    <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" />
+
+
+    <conditional name="param_type">
+    <param name="param_type_selector" type="select" label="Choose the type of parameters">
+        <option value="locarna">LocARNA defaults</option>
+        <option value="gclust" selected="True">GrapClust defaults(changeable)</option>
+    </param>
+    <when value="gclust">
+
+      <param name="p" type="float" value="0.001" size="5" label="minimal probability" help="-p"/>
+      <param name="max_diff_am" type="integer" value="50" size="5" label=" maximal difference for sizes of matched arcs" help="--max-diff-am"/>
+      <param argument="tau" type="integer" value="50" min="0" max="200" label="Sequence contribution at structure match in percent"/>
+      <param name="max_diff" type="integer" value="100" size="5" label="maximal difference for alignment traces" help="--max-diff"/>
+      <param name="plfold_minlen" type="integer" value="210" size="5" label="Minimal length of a sequences for which RNAplfold is used" />
+
+      <param name="struct_weight" argument="struct-weight"
+              label="Structure weight" type="integer"
+              value="180" min="0" max="800" />
+       <param name="indel_opening" argument="indel-opening"
+              label="Indel opening score" type="integer"
+              value="-400" max="0" min="-1500" />
+       <param argument="indel" label="Indel score" type="integer"
+              value="-200" min="-1000" max="0" />
+
+       <param  name="alifold_consensus_dp"
+               type="boolean" checked="True"
+               truevalue="--alifold-consensus-dp" falsevalue=" "
+               label="Compute consensus dot plot by alifold" />
+
+       <param name="plfold_span"
+                type="integer" value="150" min="-1" max="400"
+                label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" />
 
-		<data name="model_tree_stk" format="stockholm" label="model.tree.stk" from_work_dir="MODEL/best_subtree.aln" />
-	</outputs>
-	<tests>
-		<test>
-			<param name="tree_file" value="1.1.tree"/>
-			<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="p" value="0.001"/>
-			<param name="max-diff-am" value="50"/>
-			<param name="tau" value="50"/>
-			<param name="max-diff-am" value="100"/>
-			<output name="model_tree_stk" file="best_subtree.aln"/>
-		</test>
-	</tests>
-	<help>
-		<![CDATA[
+         <param name="plfold_winsize"
+                type="integer" value="300"  min="-1" max="800"
+                label="Window size for local folding" />
+
+
+    </when>
+    <when value="locarna">
+    </when>
+</conditional>
+
+  </inputs>
+  <outputs>
+
+    <data name="model_tree_stk" format="stockholm" label="model.tree.stk" from_work_dir="MODEL/best_subtree.aln" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="tree_file" value="1.1.tree"/>
+      <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"/>
+      <conditional name="param_type">
+        <param name="iteration_num_selector" value="gclust"/>
+        <param name="p" value="0.001"/>
+        <param name="max_diff_am" value="50"/>
+        <param name="tau" value="50"/>
+        <param name="max_diff" value="100"/>
+        <param name="plfold_minlen" value="210"/>
+        <param name="struct_weight" value="180"/>
+        <param name="indel_opening" value="-400"/>
+        <param name="indel" value="-200"/>
+        <param name="alifold_consensus_dp" value="--alifold-consensus-dp"/>
+        <param name="plfold_span" value="150"/>
+        <param name="plfold_winsize" value="300"/>
+      </conditional>
+      <output name="model_tree_stk" file="best_subtree.aln"/>
+    </test>
+  </tests>
+  <help>
+    <![CDATA[
 **What it does**
 
 MLocARNA computes a multiple sequence-structure alignment of RNA sequences.
@@ -53,9 +114,9 @@
 
 
 ]]>
-	</help>
-	<citations>
-		<citation type="bibtex">@inproceedings{costa2010fast,
+  </help>
+  <citations>
+    <citation type="bibtex">@inproceedings{costa2010fast,
         title={Fast neighborhood subgraph pairwise distance kernel},
         author={Costa, Fabrizio and De Grave, Kurt},
         booktitle={Proceedings of the 26th International Conference on Machine Learning},
@@ -64,22 +125,22 @@
         organization={Omnipress}
       }
       </citation>
-			<citation type="bibtex">@Article{Will_Joshi_Hofacker-LocAR_Accur_bound-2012,
-  author =	 {Will, Sebastian and Joshi, Tejal and Hofacker, Ivo L. and
+      <citation type="bibtex">@Article{Will_Joshi_Hofacker-LocAR_Accur_bound-2012,
+  author =   {Will, Sebastian and Joshi, Tejal and Hofacker, Ivo L. and
                   Stadler, Peter F. and Backofen, Rolf},
-  title =	 {{LocARNA}-{P}: {Accurate} boundary prediction and improved
+  title =   {{LocARNA}-{P}: {Accurate} boundary prediction and improved
                   detection of structural {RNAs}},
-  journal =	 {RNA},
-  year =	 {2012},
-  volume =	 {18},
-  number =	 {5},
-  pages =	 {900-14},
-  user =	 {will},
-  pmid =	 {22450757},
-  doi = 	 {10.1261/rna.029041.111},
-  issn = 	 {1469-9001},
-  issn = 	 {1355-8382},
-  abstract =	 {Current genomic screens for noncoding RNAs (ncRNAs) predict
+  journal =   {RNA},
+  year =   {2012},
+  volume =   {18},
+  number =   {5},
+  pages =   {900-14},
+  user =   {will},
+  pmid =   {22450757},
+  doi =    {10.1261/rna.029041.111},
+  issn =    {1469-9001},
+  issn =    {1355-8382},
+  abstract =   {Current genomic screens for noncoding RNAs (ncRNAs) predict
                   a large number of genomic regions containing potential
                   structural ncRNAs. The analysis of these data requires
                   highly accurate prediction of ncRNA boundaries and
@@ -110,14 +171,14 @@
                   for refining screens for structural ncRNA, at
                   http://www.bioinf.uni-freiburg.de/Supplements/LocARNA-P/.}
 }
-				</citation>
-				<citation type="bibtex">@Article{Will:etal:_infer_non_codin_rna_famil:PLOS2007,
-  author =	 {Sebastian Will and Kristin Reiche and Ivo L. Hofacker and
+        </citation>
+        <citation type="bibtex">@Article{Will:etal:_infer_non_codin_rna_famil:PLOS2007,
+  author =   {Sebastian Will and Kristin Reiche and Ivo L. Hofacker and
                   Peter F. Stadler and Rolf Backofen},
-  title =	 {Inferring Non-Coding {RNA} Families and Classes by Means of
+  title =   {Inferring Non-Coding {RNA} Families and Classes by Means of
                   Genome-Scale Structure-Based Clustering},
-  journal =	 {PLoS Comput Biol},
-  year =	 2007,
+  journal =   {PLoS Comput Biol},
+  year =   2007,
   volume =       {3},
   number =       {4},
   pages =        {e65},
@@ -125,8 +186,8 @@
   issn =         {1553-734X},
   pmid =         {17432929},
   doi =          {10.1371/journal.pcbi.0030065},
-  user =	 {will},
-  abstract =	 {The RFAM database defines families of ncRNAs by means of
+  user =   {will},
+  abstract =   {The RFAM database defines families of ncRNAs by means of
                   sequence similarities that are sufficientto establish
                   homology. In some cases, such as microRNAs, box H/ACA
                   snoRNAs, functional commonalities define classes of RNAs
@@ -160,23 +221,23 @@
                   characterized.}
 }
 
-					</citation>
-					<citation type="bibtex">@Article{Smith:Heyne:Richter:Freib_RNA_Tools:NAR2010,
-  author =	 {Smith, Cameron and Heyne, Steffen and Richter, Andreas S.
+          </citation>
+          <citation type="bibtex">@Article{Smith:Heyne:Richter:Freib_RNA_Tools:NAR2010,
+  author =   {Smith, Cameron and Heyne, Steffen and Richter, Andreas S.
                   and Will, Sebastian and Backofen, Rolf},
-  title =	 {Freiburg {RNA} {Tools}: a web server integrating {IntaRNA},
+  title =   {Freiburg {RNA} {Tools}: a web server integrating {IntaRNA},
                   {ExpaRNA} and {LocARNA}},
-  journal =	 NAR,
-  year =	 {2010},
-  volume =	 {38 Suppl},
-  number =	 {},
-  pages =	 {W373-7},
-  user =	 {arichter},
-  pmid =	 {20444875},
-  doi = 	 {10.1093/nar/gkq316},
-  issn = 	 {0305-1048},
-  issn =	 {1362-4962},
-  abstract =	 {The Freiburg RNA tools web server integrates three tools
+  journal =   NAR,
+  year =   {2010},
+  volume =   {38 Suppl},
+  number =   {},
+  pages =   {W373-7},
+  user =   {arichter},
+  pmid =   {20444875},
+  doi =    {10.1093/nar/gkq316},
+  issn =    {0305-1048},
+  issn =   {1362-4962},
+  abstract =   {The Freiburg RNA tools web server integrates three tools
                   for the advanced analysis of RNA in a common web-based user
                   interface. The tools IntaRNA, ExpaRNA and LocARNA support
                   the prediction of RNA-RNA interaction, exact RNA matching
@@ -185,6 +246,6 @@
                   tools are freely accessible at
                   http://rna.informatik.uni-freiburg.de.}
 }
-						</citation>
-	</citations>
+            </citation>
+  </citations>
 </tool>