--- a/fetch_fasta_from_NCBI.xml	Sun Oct 15 20:13:13 2017 -0400
+++ b/fetch_fasta_from_NCBI.xml	Wed Nov 08 13:00:26 2017 -0500
@@ -1,16 +1,12 @@
-<tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="2.1.1">
+<tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="2.2.1">
   <description></description>
   <command><![CDATA[
       python '$__tool_directory__'/fetch_fasta_from_NCBI.py
       -i "$queryString"
       -d $dbname
-      -o '$outfilename'
       -l '$logfile'
-      #if $date_condition.date_filter == "YES":
-          --datetype $date_condition.datetype
-          --mindate $date_condition.mindate
-          --maxdate $date_condition.maxdate
-      #end if
+      $dry_run
+      -o '$outfile'
   ]]></command>
 
   <inputs>
@@ -30,21 +26,12 @@
       <option value="nuccore">Nucleotide</option>
       <option value="protein">Protein</option>
     </param>
-    <conditional name="date_condition">
-        <param name="date_filter" type="boolean" label="Filter the sequences by date?" truevalue="YES" falsevalue="NO" checked="false"/>
-        <when value="YES">
-            <param name="datetype" type="select">
-                <option value="pdat">Publication date</option>
-                <option value="mdat">Modification date</option>
-            </param>
-            <param name="mindate" type="text" help="Date must follow one of the following formats: YYYY/MM/DD, YYYY/MM or YYYY"/>
-            <param name="maxdate" type="text" help="Date must follow one of the following formats: YYYY/MM/DD, YYYY/MM or YYYY"/>
-        </when>
-        <when value="NO"/>
-    </conditional>
+    <param name="dry_run" type="boolean" label="Dry run to get the number of sequences?" truevalue="--count" falsevalue="" checked="false"/>
   </inputs>
   <outputs>
-    <data name="outfilename" format="fasta" label="${tool.name} (${dbname.value_label}) with queryString '${queryString.value}'" />
+    <data name="outfile" format="fasta" label="${tool.name} (${dbname.value_label}) with queryString '${queryString.value}'" >
+      <filter> dry_run == False</filter>
+    </data>
     <data format="txt" name="logfile" label="${tool.name}: log"/>
   </outputs>
   <tests>
@@ -52,16 +39,13 @@
         <param name="queryString" value="9629650[gi]" />
         <param name="dbname" value="nuccore" />
         <output name="outfilename" ftype="fasta" file="output.fa" />
-        <!--  <output name="logfile" ftype="txt" file="log.txt" />  log.txt changes with timestamp. removed to pass the  test -->
     </test>
     <test>
         <param name="queryString" value="CU929326[Accession]" />
         <param name="dbname" value="nuccore" />
-        <param name="date_filter" value="YES"/>
-        <param name="datetype" value="pdat"/>
-        <param name="mindate" value="2008/09"/>
-        <param name="maxdate" value="2008/09"/>
-        <output name="outfilename" ftype="fasta" file="zebra_output.fa" />
+        <param name="date_filter" value="1"/>
+        <param name="dry_run" value="True"/>
+        <output name="logfile" ftype="txt" file="dry_run.log" compare="sim_size"/>
     </test>
   </tests>
   <help>