# HG changeset patch
# User rnateam
# Date 1485038361 18000
# Node ID 4310ac018d05a04cd0a70e5f1962fc96dee2099d
# Parent  4a9754d476fe56157d3ba6e67998014982fdb485
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86

diff -r 4a9754d476fe -r 4310ac018d05 evaluation.py
--- a/evaluation.py	Fri Jan 13 16:59:29 2017 -0500
+++ b/evaluation.py	Sat Jan 21 17:39:21 2017 -0500
@@ -2,6 +2,7 @@
 from os import system
 import re
 from sklearn import metrics
+from shutil import make_archive
 
 def sh(script):
     system("bash -c '%s'" % script)
@@ -67,3 +68,6 @@
 
 with open("RESULTS/evaluation.txt", "w") as fOut:
     fOut.write(toWrite)
+
+
+make_archive('RESULTS', 'zip', root_dir='RESULTS')
diff -r 4a9754d476fe -r 4310ac018d05 glob_report.xml
--- a/glob_report.xml	Fri Jan 13 16:59:29 2017 -0500
+++ b/glob_report.xml	Sat Jan 21 17:39:21 2017 -0500
@@ -1,19 +1,19 @@
 <tool id="glob_report" name="Report_Results" version="0.1">
-	<requirements>
-		<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:" />
-	</stdio>
-	<command>
-		<![CDATA[
+  <requirements>
+    <requirement type="package" version="0.1.7">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:" />
+  </stdio>
+  <command>
+    <![CDATA[
         unzip $FASTA  &> /dev/null &&
 
         #set $inputFiles = ""
@@ -29,7 +29,7 @@
             #set $inputFilesTrees += str($mods)+','
         #end for
         #set $inputFilesTrees = $inputFilesTrees[:-1]
-		    glob_res.pl
+        'glob_res.pl'
                 '$inputFiles'
                 $merge_cluster_ol
                 $merge_overlap
@@ -47,110 +47,169 @@
           $final_partition_used_cmsearch
         #end if
 
+        #if  str($advanced_opts.advanced_opts_selector) == "show":
+            #if  str($advanced_opts.param_type.param_type_selector) == "gclust":
+                  $advanced_opts.param_type.p
+                  $advanced_opts.param_type.max_diff_am
+                  $advanced_opts.param_type.max_diff
+                  $advanced_opts.param_type.tau
+                  $advanced_opts.param_type.struct_weight
+                  $advanced_opts.param_type.indel_opening
+                  $advanced_opts.param_type.indel
+                  $advanced_opts.param_type.alifold_consensus_dp
+            #end if
+        #end if
+
         &&
         python '$__tool_directory__/evaluation.py'
-		#if $cdhit:
-    		&&
-	    	python '$__tool_directory__/addCdhitseqs.py' '$cdhit'
-	    #end if
+    #if $cdhit:
+        &&
+        python '$__tool_directory__/addCdhitseqs.py' '$cdhit'
+      #end if
 ]]>
-	</command>
-	<inputs>
-		<param type="data" name="FASTA" format="zip" />
-		<param type="data" name="cmsearch_results" format="tabular" multiple="True"/>
-		<param type="data" name="model_tree_files" format="txt" multiple="True"/>
-		<param name="partition_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Hard partition"/>
-		<param name="cut_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Use CM score for cutoff" help="otherwise use E-value"/>
-		<param type="data" name="cdhit" format="txt" optional="true"/>
-		<conditional name="iteration_num">
-			<param name="iteration_num_selector" type="boolean"  checked="no" label="Multiple iterations"  help="for single iteration- NO, for multiple-YES"/>
-			<when value="true">
-				<param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/>
-				<param type="data" name="final_partition_soft" format="txt" />
-				<param type="data" name="final_partition_used_cmsearch" format="txt" />
-			</when>
-			<when value="false" ></when>
-		</conditional>
-		<param name="merge_cluster_ol" type="float" value="0.66" size="5" label="merge_cluster_ol" help=""/>
-		<param name="merge_overlap" type="float" value="0.51" size="5" label="merge_overlap" help=""/>
-		<param name="min_cluster_size" type="integer" value="3" size="5" label="min_cluster_size" help=""/>
-		<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"  />
-		<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>
-			<param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/>
-			<param name="cmsearch_results" value="1.tabular,2.tabular"/>
-			<param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/>
-			<param name="partition_type" value="0"/>
-			<param name="cut_type" value="0"/>
-			<conditional name="iteration_num">
-				<param name="iteration_num_selector" value="false"/>
-			</conditional>
-			<param name="merge_cluster_ol" value="0.66"/>
-			<param name="merge_overlap" value="0.51"/>
-			<param name="min_cluster_size" value="3"/>
-			<param name="cm_min_bitscore" value="20"/>
-			<param name="cm_max_eval" value="0.001"/>
-			<param name="cm_bitscore_sig" value="1"/>
-			<output name="final_stats" file="RESULTS/cluster.final.stats" />
-			<output_collection name="clusters" type="list">
-				<element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/>
-				<element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/>
-			</output_collection>
-			<output_collection name="partitions">
-				<element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains">
-					<assert_contents>
-						<has_text text="1.1  1.1" />
-						<has_text text="1.2  1.2" />
-					</assert_contents>
-				</element>
-				<element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains">
-					<assert_contents>
-						<has_text text="MODEL CLASS 0 0" />
-						<has_text text="1.2" />
-						<has_text text="1.1" />
-					</assert_contents>
-				</element>
-				<element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" />
-				<element name="final_partition.hard.merged" file="RESULTS/partitions/final_partition.hard.merged" />
-				<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>
-		<![CDATA[
+  </command>
+  <inputs>
+    <param type="data" name="FASTA" format="zip" />
+    <param type="data" name="cmsearch_results" format="tabular" multiple="True"/>
+    <param type="data" name="model_tree_files" format="txt" multiple="True"/>
+    <param name="partition_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Hard partition"/>
+    <param name="cut_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Use CM score for cutoff" help="otherwise use E-value"/>
+    <param type="data" name="cdhit" format="txt" optional="true"/>
+    <conditional name="iteration_num">
+      <param name="iteration_num_selector" type="boolean"  checked="no" label="Multiple iterations"  help="for single iteration- NO, for multiple-YES"/>
+      <when value="true">
+        <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/>
+        <param type="data" name="final_partition_soft" format="txt" />
+        <param type="data" name="final_partition_used_cmsearch" format="txt" />
+      </when>
+      <when value="false" ></when>
+    </conditional>
+    <param name="merge_cluster_ol" type="float" value="0.66" size="5" label="merge_cluster_ol" help=""/>
+    <param name="merge_overlap" type="float" value="0.51" size="5" label="merge_overlap" help=""/>
+    <param name="min_cluster_size" type="integer" value="3" size="5" label="min_cluster_size" help=""/>
+    <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=""/>
+
+    <conditional name="advanced_opts">
+    <param name="advanced_opts_selector" type="select" label="Advanced Options">
+        <option value="hide" selected="True">Hide</option>
+        <option value="show">Show</option>
+    </param>
+    <when value="hide"></when>
+    <when value="show">
+
+      <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="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" />
+
+      </when>
+      <when value="locarna">
+      </when>
+  </conditional>
+
+    </when>
+  </conditional>
+
+  </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"  />
+    <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>
+    <data name="RESULTS_zip" format="zip" from_work_dir="RESULTS.zip" label="RESULTS.zip"  />
+  </outputs>
+  <tests>
+    <test>
+      <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/>
+      <param name="cmsearch_results" value="1.tabular,2.tabular"/>
+      <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/>
+      <param name="partition_type" value="0"/>
+      <param name="cut_type" value="0"/>
+      <conditional name="iteration_num">
+        <param name="iteration_num_selector" value="false"/>
+      </conditional>
+      <param name="merge_cluster_ol" value="0.66"/>
+      <param name="merge_overlap" value="0.51"/>
+      <param name="min_cluster_size" value="3"/>
+      <param name="cm_min_bitscore" value="20"/>
+      <param name="cm_max_eval" value="0.001"/>
+      <param name="cm_bitscore_sig" value="1"/>
+      <output name="final_stats" file="RESULTS/cluster.final.stats" />
+      <output_collection name="clusters" type="list">
+        <element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/>
+        <element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/>
+      </output_collection>
+      <output_collection name="partitions">
+        <element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains">
+          <assert_contents>
+            <has_text text="1.1  1.1" />
+            <has_text text="1.2  1.2" />
+          </assert_contents>
+        </element>
+        <element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains">
+          <assert_contents>
+            <has_text text="MODEL CLASS 0 0" />
+            <has_text text="1.2" />
+            <has_text text="1.1" />
+          </assert_contents>
+        </element>
+        <element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" />
+        <element name="final_partition.hard.merged" file="RESULTS/partitions/final_partition.hard.merged" />
+        <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>
+      <output name="RESULTS_zip" file="RESULTS.zip" ftype="zip" compare="sim_size" />
+
+    </test>
+  </tests>
+  <help>
+    <![CDATA[
 
 **What it does**
 
@@ -160,8 +219,8 @@
 Cluster members are finally ranked by their CM bitscore.
 
     ]]>
-	</help>
-	<citations>
+  </help>
+  <citations>
     <citation type="bibtex">@inproceedings{costa2010fast,
         title={Fast neighborhood subgraph pairwise distance kernel},
         author={Costa, Fabrizio and De Grave, Kurt},
diff -r 4a9754d476fe -r 4310ac018d05 test-data/RESULTS.zip
Binary file test-data/RESULTS.zip has changed