--- a/repex_tarean.xml	Wed Jan 08 06:31:13 2020 -0500
+++ b/repex_tarean.xml	Mon Feb 03 02:34:46 2020 -0500
@@ -73,8 +73,8 @@
   </command>
 
   <inputs>
-	  <param name="FastaFile" label="paired-end NGS reads" type="data" format="fasta"
-	         help="Input file must contain fasta-formatted interlaced read pairs from paired-end sequencing. All pairs must be complete. Example of input data format is provided in the help below."/>
+	  <param name="FastaFile" label="Paired-end Illumina reads" type="data" format="fasta"
+	         help="Input file must contain FASTA-formatted interlaced read pairs from paired-end sequencing. All pairs must be complete. Example of the input data format is provided in the help below."/>
 	  <param name="sample" label="Sample size" type="integer" value="500000" min="10000"/>
 
     <conditional name="advanced_options">
@@ -93,11 +93,11 @@
 	          <param name="library" format="fasta" type="data" label="Use custom repeat database" help="Perform additional similarity search to user-provided repeat database. The database should contain FASTA-formatted DNA sequences with headers (sequence names) in the format: '>reapeatname#class/subclass'"/>
           </when>
         </conditional>
-        <param name="size_threshold" label="Cluster size threshold  for detailed analysis" type="float" value="0.01" min="0.0001" max="100" help ="Minimal size (as percentage of input reads) of the smallest cluster which is analyzed, cluster with less than 20 reads are not considered at all."/>
+        <param name="size_threshold" label="Cluster size threshold for detailed analysis" type="float" value="0.01" min="0.0001" max="100" help ="Minimal size (as percentage of input reads) of the smallest cluster which is analyzed; cluster with less than 20 reads are not considered."/>
         <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/>
-        <param name="keep_names" label="Keep original sequences names" type="boolean" truevalue="--keep_names" falsevalue="" checked="false" help="By default sequence are relabeled using  integers. If you want to keep original names, use this option."/>
+        <param name="keep_names" label="Keep original read names" type="boolean" truevalue="--keep_names" falsevalue="" checked="false" help="By default, reads are renamed using integers. Use this option if you want to keep original names."/>
          <conditional name="options">
-           <param name="options" type="select" label="Similarity search options" help="Different similarity search parameters are used depending on the used input data to adjust search to differences in length and error rate">
+           <param name="options" type="select" label="Similarity search options" help="Different similarity search parameters are used depending on the input data to adjust search to differences in read length and error rate">
              <option value="ILLUMINA" selected="true">Illumina reads, read length 100nt or more </option>
              <option value="ILLUMINA_SHORT" selected="false">Illumina reads, shorter than 100nt (Do not use reads shorter than 50nt!) </option>
              <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats  </option>
@@ -108,9 +108,9 @@
 
          <conditional name="queue_definition">
                <param name="queue_select" type="select" label="Select queue">
-                 <option value="basic_fast_queue">basic &amp; fast</option>
-                 <option value="long_slow_queue">long &amp; slow</option>
-                 <option value="extra_long_slow_queue">extra long &amp; slow</option>
+                 <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option>
+                 <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option>
+                 <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option>
                </param>
                <when value="basic_fast_queue">
                  <param name="queue_specification" type="text" label="Modify parameters (optional)"