--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_comparative_clustering_summary.xml	Wed Apr 28 08:37:20 2021 +0000
@@ -0,0 +1,71 @@
+<tool id="plot_comparative" name="Visualization of comparative clustering" version="1.0.0">
+  <description> Simple utility to create visualization of RepeatExplorer conmparative analysis</description>
+  <requirements>
+    <requirement type="package">r-optparse</requirement>
+  </requirements>
+  
+    <command interpreter="Rscript" detect_errors="exit_code" >
+    $__tool_directory__/plot_comparative_clustering_summary.R
+    --cluster_table=$cluster_table
+    --comparative_counts=$counts
+    --number_of_colors=$number_of_colors
+    --output=$outpdf
+    $nuclear_only
+
+    #if $normalization.use_genome_size:
+      --genome_size $normalization.genome_size_table
+    #end if
+    </command>
+
+    <inputs>
+      <param format="txt" type="data" name="cluster_table" label="file from RepeatExplorer2 clustering - CLUSTER_TABLE.csv"/>
+      <param format="txt" type="data" name="counts" label="file from RepeatExplorer2 output - COMPARATIVE_ANALYSIS_COUNTS.csv"/>
+      <param value="10" min="2" max="20" type="integer" name="number_of_colors" label="Maximum number of color used for plottting"/>
+      <param value="false"  type="boolean" truevalue="--nuclear_only" falsevalue="" name="nuclear_only" label="Remove all non-nuclear sequences (organel and contamination)"/>
+      <conditional name="normalization">
+        <param name="use_genome_size" type="boolean" checked="False" label="Normalize to genome size" help="Note that if this option is used, non-nuclear sequences are always removed."/>
+        <when value="false">
+          <!-- pass -->
+        </when>
+        <when value="true">
+          <param name="genome_size_table" type="data" format="txt" label="table with genome sizes"/>
+
+        </when>
+
+      </conditional>
+    </inputs>
+
+    <outputs>
+         	<data format="pdf" name="outpdf" label="Comparative analysis summary"/>
+    </outputs>
+    <help>
+      **Visualization of comparative clustering**
+      Visualization can be created two output files from RepeatExplorer pipeline.
+      
+      Input file CLUSTER_TABLE.csv contains automatic annotation, information about cluster sizes and the total number of reads used for analysis
+      Example of CLUSTER_TABLE.csv: ::
+
+          "Number_of_reads_in_clusters"	3002
+          "Number_of_clusters"	895
+          "Number_of_superclusters"	895
+          "Number_of_singlets"	6998
+
+          "Number_of_analyzed_reads"	10000
+          
+          "Cluster"	"Supercluster"	"Size"	"Size_adjusted"	"Automatic_annotation"	"TAREAN_classification"	"Final_annotation"
+          1	1	61	61	"All"	"Other"
+          2	2	59	59	"All/repeat/satellite"	"Putative satellites (high confidence)"
+          3	3	45	45	"All/repeat/satellite"	"Putative satellites (low confidence)"
+          4	4	38	38	"All"	"Other"
+          5	5	32	32	"All"	"Other"
+          6	6	28	28	"All"	"Other"
+          7	7	25	25	"All"	"Other"
+          8	8	24	24	"All"	"Other"
+          9	9	23	23	"All"	"Other"
+          10	10	22	22	"All/repeat/mobile_element/Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre"	"Other"
+          11	11	20	20	"All"	"Other"
+          12	12	20	20	"All"	"Other"
+
+
+    </help>
+</tool>