--- a/summarize_cluster_table.xml	Thu Jul 27 09:46:13 2023 +0000
+++ b/summarize_cluster_table.xml	Wed Aug 02 11:31:12 2023 +0000
@@ -1,42 +1,58 @@
-<tool id="summarize_annotation" name="Repeat proportions from CLUSTER_TABLE" version="1.0.0">
-  <description> Simple utility to summarize final annotations from RepeatExplorer CLUSTER_TABLE</description>
-  <requirements>
-    <requirement type="package">r-optparse</requirement>
-  </requirements>
-  
-    <command interpreter="Rscript" detect_errors="exit_code" >
-    $__tool_directory__/summarize_cluster_table.R
-    --cluster_table=$cluster_table
-    --output=$output
+<tool id="summarize_annotation" name="Repeat proportions from CLUSTER_TABLE"
+      version="1.0.0.3">
+    <description>Simple utility to summarize final annotations from RepeatExplorer
+        CLUSTER_TABLE
+    </description>
+    <requirements>
+        <requirement type="package">r-optparse</requirement>
+    </requirements>
+    <required_files>
+        <include type="literal" path="summarize_cluster_table.R"/>
+    </required_files>
+    <command interpreter="Rscript" detect_errors="exit_code">
+        Rscript $__tool_directory__/summarize_cluster_table.R
+        --cluster_table=$cluster_table
+        --output=$output
 
     </command>
 
     <inputs>
-      <param format="txt" type="data" name="cluster_table" label="file from RepeatExplorer2 clustering - CLUSTER_TABLE.csv" help="CLUSTER_TABLE.csv must contains completed Final_annotation column" />
+        <param format="txt" type="data" name="cluster_table"
+               label="file from RepeatExplorer2 clustering - CLUSTER_TABLE.csv"
+               help="CLUSTER_TABLE.csv must contains completed Final_annotation column"/>
     </inputs>
 
     <outputs>
-         	<data format="tabular" name="output" label="Summary of repeat proportions from ${cluster_table.hid}"/>
+        <data format="tabular" name="output"
+              label="Summary of repeat proportions from ${cluster_table.hid}"/>
     </outputs>
     <help>
-      **The tool calculates genome proportions of identified repeats based on cluster annotations in CLUSTER_TABLE.csv**
-          
-	  The column "Final_annotation" must be filled in the input file CLUSTER_TABLE.csv. Contamination and organelle clusters are discarded from quantification. Table header with information about numbers of analyzed reads should remain unchanged - see example below.
+        **The tool calculates genome proportions of identified repeats based on cluster
+        annotations in CLUSTER_TABLE.csv**
 
-      Example of CLUSTER_TABLE.csv: ::
+        The column "Final_annotation" must be filled in the input file CLUSTER_TABLE.csv.
+        Contamination and organelle clusters are discarded from quantification. Table
+        header with information about numbers of analyzed reads should remain unchanged -
+        see example below.
+
+        Example of CLUSTER_TABLE.csv: ::
 
-          Number_of_reads_in_clusters	1185180					
-          Number_of_clusters	62148					
-          Number_of_superclusters	62031					
-          Number_of_singlets	314820					
-          Number_of_analyzed_reads	1500000					
-          Cluster	Supercluster	Size	Size_adjusted	Automatic_annotation	TAREAN_annotation	Final_annotation						
-          10	4	11967	11967	All/repeat/mobile_element/Class_I/LTR/Ty1_copia/SIRE	Other	All/repeat/mobile_element/Class_I/LTR/Ty1_copia/SIRE
-          137	5	2094	2094	All/repeat	Other	All/repeat
-          112	9	3117	3117	All/repeat/rDNA/45S_rDNA	Other	All/repeat/rDNA/45S_rDNA
-          16	11	10078	10078	All/repeat/satellite	Putative satellites (high confidence)	All/repeat/satellite
-          125	22	2630	2630	All/organelle/plastid	Other	All/organelle/plastid
-          124	40	2645	2645	All/repeat/mobile_element/Class_I/LTR/Ty1_copia/Ivana	Putative LTR elements	All/repeat/mobile_element/Class_I/LTR/Ty1_copia/Ivana
+        Number_of_reads_in_clusters 1185180
+        Number_of_clusters 62148
+        Number_of_superclusters 62031
+        Number_of_singlets 314820
+        Number_of_analyzed_reads 1500000
+        Cluster Supercluster Size Size_adjusted Automatic_annotation TAREAN_annotation
+        Final_annotation
+        10 4 11967 11967 All/repeat/mobile_element/Class_I/LTR/Ty1_copia/SIRE Other
+        All/repeat/mobile_element/Class_I/LTR/Ty1_copia/SIRE
+        137 5 2094 2094 All/repeat Other All/repeat
+        112 9 3117 3117 All/repeat/rDNA/45S_rDNA Other All/repeat/rDNA/45S_rDNA
+        16 11 10078 10078 All/repeat/satellite Putative satellites (high confidence)
+        All/repeat/satellite
+        125 22 2630 2630 All/organelle/plastid Other All/organelle/plastid
+        124 40 2645 2645 All/repeat/mobile_element/Class_I/LTR/Ty1_copia/Ivana Putative
+        LTR elements All/repeat/mobile_element/Class_I/LTR/Ty1_copia/Ivana
 
     </help>
 </tool>