# HG changeset patch
# User rnateam
# Date 1484344769 18000
# Node ID 4a9754d476fe56157d3ba6e67998014982fdb485
# Parent  79b9117aef0158b410cbe13f1ef2808b7ea120b0
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 287021573c592fdb70fdbbc88943aa16a8740fc0

diff -r 79b9117aef01 -r 4a9754d476fe glob_report.xml
--- a/glob_report.xml	Wed Jan 04 18:15:07 2017 -0500
+++ b/glob_report.xml	Fri Jan 13 16:59:29 2017 -0500
@@ -3,6 +3,11 @@
 		<requirement type="package" version="0.1">graphclust-wrappers</requirement>
 		<requirement type="package" version='0.5'>perl-array-utils</requirement>
 		<requirement type="package" version='0.18.1'>scikit-learn</requirement>
+		<requirement type="package" version='1.8.10'>locarna</requirement>
+		<requirement type="package" version='2.1'>rnaz</requirement>
+		<requirement type="package" version="1.1">infernal</requirement>
+		<requirement type="package" version='2.2.10'>viennarna</requirement>
+		<requirement type="package" version='1.3.23'>graphicsmagick</requirement>
 	</requirements>
 	<stdio>
 		<exit_code range="1:" />
@@ -24,7 +29,7 @@
             #set $inputFilesTrees += str($mods)+','
         #end for
         #set $inputFilesTrees = $inputFilesTrees[:-1]
-		    glob_res.pl 
+		    glob_res.pl
                 '$inputFiles'
                 $merge_cluster_ol
                 $merge_overlap
@@ -35,6 +40,7 @@
                 $partition_type ''
                 $cut_type
                 '$inputFilesTrees'
+                $results_top_num
         #if  $iteration_num.iteration_num_selector:
           $iteration_num.CI
           $final_partition_soft
@@ -46,7 +52,7 @@
 		#if $cdhit:
     		&&
 	    	python '$__tool_directory__/addCdhitseqs.py' '$cdhit'
-	    #end if		
+	    #end if
 ]]>
 	</command>
 	<inputs>
@@ -71,19 +77,26 @@
 		<param name="cm_min_bitscore" type="integer" value="20" size="5" label="cm_min_bitscore" help=""/>
 		<param name="cm_max_eval" type="float" value="0.001" size="5" label="cm_max_eval" help=""/>
 		<param name="cm_bitscore_sig" type="integer" value="1" size="5" label="cm_bitscore_sig" help=""/>
+		<param name="results_top_num" type="integer" value="5" size="5" label="results_top_num" help=""/>
 	</inputs>
 	<outputs>
 		<data name="final_stats" format="txt" from_work_dir="RESULTS/cluster.final.stats" label="cluster.final.stats"  />
 		<data name="tableForEval" format="tabular" from_work_dir="RESULTS/fullTab.tabular" label="tableForEval"  />
 		<data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part"   />
 		<data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch"   />
-		<data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters"   />
+		<data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters"  />
 		<collection name="clusters" type="list" label="CLUSTERS">
 			<discover_datasets pattern="(?P&lt;name&gt;^.*\.all$)" directory="RESULTS"  />
 		</collection>
 		<collection name="partitions" type="list" label="Partitions">
 			<discover_datasets pattern="(?P&lt;name&gt;^.*$)" directory="RESULTS/partitions" />
 		</collection>
+		<collection name="topSecondaryStruct" type="list" label="Top $results_top_num alirna.ps">
+			<discover_datasets format="png" pattern="(?P&lt;name&gt;^.*\.alirna.png$)"  />
+		</collection>
+		<collection name="topDot" type="list" label="Top $results_top_num aln.ps">
+			<discover_datasets format="png" pattern="(?P&lt;name&gt;^.*\.aln.png$)"  />
+		</collection>
 	</outputs>
 	<tests>
 		<test>
@@ -125,6 +138,15 @@
 				<element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" />
 				<element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/>
 			</output_collection>
+			<param name="results_top_num" value="5"/>
+			<output_collection name="topSecondaryStruct" type="list">
+				<element name="1.cluster.top5.alirna.png" file="1.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
+				<element name="2.cluster.top5.alirna.png" file="2.cluster.top5.alirna.png" ftype="png" compare="sim_size" />
+			</output_collection>
+			<output_collection name="topDot" type="list">
+				<element name="1.cluster.top5.aln.png" file="1.cluster.top5.aln.png"  ftype="png" compare="sim_size"/>
+				<element name="2.cluster.top5.aln.png" file="2.cluster.top5.aln.png"  ftype="png" compare="sim_size"/>
+			</output_collection>
 		</test>
 	</tests>
 	<help>
diff -r 79b9117aef01 -r 4a9754d476fe test-data/1.cluster.top5.alirna.png
Binary file test-data/1.cluster.top5.alirna.png has changed
diff -r 79b9117aef01 -r 4a9754d476fe test-data/1.cluster.top5.aln.png
Binary file test-data/1.cluster.top5.aln.png has changed
diff -r 79b9117aef01 -r 4a9754d476fe test-data/2.cluster.top5.alirna.png
Binary file test-data/2.cluster.top5.alirna.png has changed
diff -r 79b9117aef01 -r 4a9754d476fe test-data/2.cluster.top5.aln.png
Binary file test-data/2.cluster.top5.aln.png has changed