--- a/filter_by_fasta_ids.xml	Fri Feb 15 16:38:31 2019 -0500
+++ b/filter_by_fasta_ids.xml	Thu Apr 18 02:45:18 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="filter_by_fasta_ids" name="Filter FASTA" version="2.1">
+<tool id="filter_by_fasta_ids" name="Filter FASTA" version="2.2">
     <description>on the headers and/or the sequences</description>
     <macros>
         <xml name="regexp_macro" token_label="Regular expression pattern">
@@ -25,8 +25,8 @@
     --id_list '$header_criteria.identifiers'
     #if $header_criteria.id_regex.find == 'pattern':
         --pattern '$header_criteria.id_regex.pattern'
-    #elif $header_criteria.id_regex.find == 'beginning':
-        --pattern '$header_criteria.id_regex.pattern'
+    #else:
+        --pattern '>([^| ]+)'
     #end if
 #elif $header_criteria.header_criteria_select == 'regexp'
     --header_regexp '$header_criteria.regexp'
@@ -56,30 +56,21 @@
             <when value="" />
             <when value="id_list">
                 <param name="identifiers" type="data" format="txt" label="List of IDs to extract sequences for"/>
-                
-                
                 <conditional name="id_regex">
-                    <param name="find" type="select" label="Match IDs by">
+                    <param name="find" type="select" label="Match IDs by"
+                        help="Default: &gt;ID will use search pattern >([^| ]+) to input ID; Use custom regex to change">
                         <option value="beginning">Default: ID is expected at the beginning: &gt;ID </option>
-                        <help>Default: &gt;ID will use search pattern >([^| ]+) to input ID; Use custom regex to change</help>
                         <option value="pattern">Custom regex pattern</option>
                     </param>
-                    <when value="beginning">
-                        <param name="pattern" type="hidden" value=">([^| ]+)" label="regex search pattern for ID" >
-                            <sanitizer sanitize="False"/>
-                            <validator type="regex" message="must include a group that returns an ID">^.*[(](?![?]:).*[)].*$</validator>
-                        </param>
-                    </when>
+                    <when value="beginning" />
                     <when value="pattern">
-                        <param name="pattern" type="text" value="" label="regex search pattern for ID">
-                            <help>search pattern must contain %s where the ID will be substituted. Use this for Uniprot Acc: >.+?\|(.+?)\|.*$ </help>
+                        <param name="pattern" type="text" value="" label="Regex search pattern for ID"
+                            help="Search pattern must contain %s where the ID will be substituted. Use this for Uniprot Acc: >.+?\|(.+?)\|.*$">
                             <sanitizer sanitize="False"/>
                             <validator type="regex" message="must include a group that returns an ID">^.*[(](?![?]:).*[)].*$</validator>
                         </param>
                     </when>
                 </conditional>
-                
-                
             </when>
             <when value="regexp">
                 <expand macro="regexp_macro" label="Regular expression pattern the header should match" />
@@ -137,8 +128,10 @@
         </test>
         <test expect_num_outputs="2">
             <param name="input" ftype="fasta" value="input.fasta" />
-            <param name="header_criteria_select" value="regexp" />
-            <param name="regexp" value="2" />
+            <conditional name="header_criteria">
+                <param name="header_criteria_select" value="regexp" />
+                <param name="regexp" value="2" />
+            </conditional>
             <param name="dedup" value="False" />
             <param name="output_discarded" value="True" />
             <output name="output" file="output_header_regexp.fasta" />
@@ -164,13 +157,30 @@
         </test>
         <test expect_num_outputs="2">
             <param name="input" ftype="fasta" value="input.fasta" />
-            <param name="sequence_criteria_select" value="regexp" />
-            <param name="regexp" value="T{2,}" />
+            <conditional name="sequence_criteria">
+                <param name="sequence_criteria_select" value="regexp" />
+                <param name="regexp" value="T{2,}" />
+            </conditional>
             <param name="dedup" value="False" />
             <param name="output_discarded" value="True" />
             <output name="output" file="output_sequence_regexp.fasta" />
             <output name="discarded" file="discarded_sequence_regexp.fasta" />
         </test>
+        <test expect_num_outputs="2">
+            <param name="input" ftype="fasta" value="input.fasta" />
+            <conditional name="header_criteria">
+                <param name="header_criteria_select" value="regexp" />
+                <param name="regexp" value="3|5" />
+            </conditional>
+            <conditional name="sequence_criteria">
+                <param name="sequence_criteria_select" value="regexp" />
+                <param name="regexp" value="ACGT" />
+            </conditional>
+            <param name="dedup" value="False" />
+            <param name="output_discarded" value="True" />
+            <output name="output" file="output_header_regexp_sequence_regexp.fasta" />
+            <output name="discarded" file="discarded_header_regexp_sequence_regexp.fasta" />
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**