--- a/bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml	Tue Mar 15 10:06:15 2022 +0000
+++ b/bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml	Tue Mar 22 12:34:36 2022 +0000
@@ -5,7 +5,7 @@
   </requirements>
   <version_command>bowtie --version</version_command>
   <command>
-    python '$__tool_directory__/bowtie_wrapper.py'
+    python '$__tool_directory__/bowtie_transcriptome_wrapper.py'
       ## Set number of threads
       --threads="\${GALAXY_SLOTS:-4}"
       ## Outputs
@@ -154,12 +154,12 @@
   </command>
   <inputs>
     <conditional name="refGenomeSource">
-      <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
+      <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in index?" help="Built-ins were indexed using default options">
         <option value="indexed">Use a built-in index</option>
         <option value="history">Use one from the history</option>
       </param>
       <when value="indexed">
-        <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
+        <param name="index" type="select" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team">
           <options from_data_table="bowtie_indexes">
             <filter type="sort_by" column="2" />
             <validator type="no_options" message="No indexes are available" />
@@ -167,7 +167,7 @@
         </param>
       </when>
       <when value="history">
-        <param name="ownFile" type="data" format="bowtie_base_index,fasta" label="Select the reference genome" />
+        <param name="ownFile" type="data" format="bowtie_base_index,fasta" label="Select the reference" />
         <conditional name="indexParams">
           <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own" help="These settings are ignored when using a prebuilt index">
             <option value="indexPreSet">Default</option>
@@ -257,7 +257,7 @@
             </param>
             <param name="sReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
               <option value="reverse">Align against the reverse-complement reference strand</option>
-              <option value="noReverse">Do not align against the reverse-complement reference strand</option>
+              <option value="noReverse" selected="true">Do not align against the reverse-complement reference strand</option>
             </param>
             <conditional name="sBestOption">
               <param name="sBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option">
@@ -340,7 +340,7 @@
             <conditional name="alignModeOption">
               <param name="alignMode" type="select" label="Alignment mode">
                 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
-                <option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option>
+                <option value="vMode" selected="true">ignore qualities, limit end-to-end mismatches (-v)</option>
               </param>
               <when value="nMode">
                 <param name="pMismatchSeed" type="integer" value="2" min="0" max="3" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
@@ -353,6 +353,7 @@
               </when>
               <when value="vMode">
                 <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
+                <param name="pSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" />
               </when>
             </conditional>
             <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />