--- a/dante_gff_output_filtering.xml	Fri Apr 03 07:27:59 2020 -0400
+++ b/dante_gff_output_filtering.xml	Wed Jan 25 13:06:55 2023 +0000
@@ -1,11 +1,16 @@
-<tool id="domains_filter" name="Protein Domains Filter" version="1.0.1">
+<tool id="domains_filter" name="Protein Domains Filter" version="1.1.4">
   <description> Tool for filtering of gff3 output from DANTE. Filtering can be performed based domain type and alignment quality. </description>
-  <stdio>
+    <requirements>
+        <requirement type="package">dante=0.1.4</requirement>
+    </requirements>
+    <stdio>
+        <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
+        <regex match="error" source="stderr" level="fatal" description="Unknown error" />
     <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
     <regex match="error" source="stderr" level="fatal" description="Unknown error" />
   </stdio>
 <command>
-python3 ${__tool_directory__}/dante_gff_output_filtering.py --dom_gff ${DomGff} --domains_prot_seq ${dom_prot_seq} --domains_filtered ${dom_filtered} --selected_dom ${selected_domain} --th_identity ${th_identity} --th_similarity ${th_similarity} --th_length ${th_length} --interruptions ${interruptions} --max_len_proportion ${th_len_ratio} --element_type '${element_type}'
+dante_gff_output_filtering.py --dom_gff ${DomGff} --domains_prot_seq ${dom_prot_seq} --domains_filtered ${dom_filtered} --selected_dom ${selected_domain} --th_identity ${th_identity} --th_similarity ${th_similarity} --th_length ${th_length} --interruptions ${interruptions} --max_len_proportion ${th_len_ratio} --element_type '${element_type}'
 		
 </command>
 <inputs>
@@ -16,10 +21,20 @@
 	<param name="interruptions" type="integer" value="3" label="Interruptions [frameshifts + stop codons]" help="Tolerance threshold per every starting 100 amino acids of alignment sequence" />
 	<param name="th_len_ratio" type="float" value="1.2" label="Maximal length proportion" help="Maximal proportion of alignment length to the original length of protein domain from database (including indels)" />
 	<param name="selected_domain" type="select" label="Select protein domain type" >
-    <options from_file="select_domain.loc" >
-     <column name="name" index="0"/>
-     <column name="value" index="0"/>
-	</options>
+        <option value="All" selected="true">All</option>
+        <option value="GAG">GAG</option>
+        <option value="INT">INT</option>
+        <option value="PROT">PROT</option>
+        <option value="RH">RH</option>
+        <option value="RT">RT</option>
+        <option value="aRH">aRH</option>
+        <option value="CHDCR">CHDCR</option>
+        <option value="CHDII">CHDII</option>
+        <option value="TPase">TPase</option>
+        <option value="YR">YR</option>
+        <option value="HEL1">HEL1</option>
+        <option value="HEL2">HEL2</option>
+        <option value="ENDO">ENDO</option>
    </param>
    <param name="element_type" type="text" value="" label="Filter based on classification" help="You can use preset options or enter an  arbitrary string to filter a certain repetitive element type of any level. It must be a continuous substring in a proper format of Final_Classification attribute of GFF3 file. Classification levels are separated by | character. Filtering is case sensitive">
      <option value="Ty1/copia">Ty1/copia</option>