--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/glob_report.xml.orig	Sat Oct 27 13:23:06 2018 -0400
@@ -0,0 +1,268 @@
+<<<<<<< HEAD
+<tool id="glob_report" name="cluster_collection_report" version="0.4" >
+=======
+<tool id="glob_report" name="cluster_collection_report" version="0.3" >
+>>>>>>> edc317491e1fdf1233bd9b45376dc05abf6eabd5
+  <requirements>
+    <requirement type="package" version="0.5.2">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="1.1.2">infernal</requirement>
+    <requirement type="package" version='2.2.10'>viennarna</requirement>
+    <requirement type="package" version='1.3.26'>graphicsmagick</requirement>
+    <requirement type="package" version='0.6.1'>rscape</requirement>
+    <requirement type="package" version='6.0'>unzip</requirement>
+    
+  </requirements>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+  <command>
+    <![CDATA[
+        unzip $FASTA  &> /dev/null &&
+
+          mkdir ./CMSEARCH &&
+          mkdir ./MODEL &&
+
+        #set $inputFiles = ""
+
+        #for $cms_res in $cmsearch_results:
+            ###set $inputFiles += str($cms_res.element_identifier)+','
+          ln -f -s  '$cms_res' ./CMSEARCH/$cms_res.element_identifier &&
+        #end for
+        #set $inputFiles = $inputFiles[:-1]
+
+        #set $inputFilesTrees = ""
+
+        #for $mods in $model_tree_files:
+            ###set $inputFilesTrees += str($mods.element_identifier)+','
+            ln -f -s  '$mods' ./MODEL/$mods.element_identifier &&
+        #end for
+        #set $inputFilesTrees = $inputFilesTrees[:-1]
+
+     
+        'glob_res.pl'
+                ##'$inputFiles'
+                $merge_cluster_ol
+                $merge_overlap
+                $min_cluster_size
+                $cm_min_bitscore
+                $cm_max_eval
+                $cm_bitscore_sig
+                $partition_type ''
+                $cut_type
+                ##'$inputFilesTrees'
+                $results_top_num
+        #if  $iteration_num.iteration_num_selector:
+          $iteration_num.CI
+          $final_partition_soft
+          $final_partition_used_cmsearch
+          '$combined_cm'
+
+        #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
+                  $advanced_opts.param_type.alifold_consensus_dp
+            #end if
+        #end if
+
+        &&
+<<<<<<< HEAD
+        python '$__tool_directory__/evaluation.py' FASTA/ RESULTS/
+=======
+        python '$__tool_directory__/evaluation.py'
+>>>>>>> edc317491e1fdf1233bd9b45376dc05abf6eabd5
+       
+    #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" />
+        <param type="data" name="combined_cm" 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"  />
+    <data name="combined_cm_out" format="txt" from_work_dir="combined_cm_out" label="combined_cmsearch_output"  />
+    <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>
+    <collection name="rscapePlot" type="list" label="R-scape Plot">
+      <discover_datasets format="pdf" pattern="(?P&lt;name&gt;^.*\.pdf$)"  />
+    </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="1.1.tree,1.2.tree"/>
+      <param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/>
+      <param name="combined_cm_out" value="combined_cm_out"/>
+      <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="0"/>
+      <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_collection name="rscapePlot" type="list">
+        <element name="1.cluster.top5.result.aln_1.R2R.sto.pdf" file="1.cluster.top5.result.aln_1.R2R.sto.pdf"  ftype="pdf" compare="sim_size" />
+        <element name="2.cluster.top5.result.aln_1.R2R.sto.pdf" file="2.cluster.top5.result.aln_1.R2R.sto.pdf"  ftype="pdf" compare="sim_size" />
+      </output_collection>
+
+      <output name="RESULTS_zip" file="RESULTS.zip" ftype="zip" compare="sim_size" delta="20000"/>
+
+    </test>
+  </tests>
+  <help>
+    <![CDATA[
+
+**What it does**
+
+Post-processing. Redundant clusters are merged and instances that belong to multiple clusters
+are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of
+instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.
+Cluster members are finally ranked by their CM bitscore.
+
+    ]]>
+  </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},
+        pages={255--262},
+        year={2010},
+        organization={Omnipress}
+      }
+      </citation>
+  </citations>
+</tool>