--- a/align_and_estimate_abundance.xml	Mon Apr 25 10:02:37 2016 -0400
+++ b/align_and_estimate_abundance.xml	Tue May 03 10:54:25 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="align_and_estimate_abundance" name="Align reads and estimate abundance" version="2.1.1">
+<tool id="align_and_estimate_abundance" name="Align reads and estimate abundance" version="2.1.1.1">
     <description>on a de novo assembly of RNA-Seq data</description>
     <requirements>
         <requirement type="package" version="2.1.1">trinity</requirement>
@@ -17,7 +17,7 @@
         &&
 
         align_and_estimate_abundance.pl
-       
+
         --transcripts input.fa
 
         --est_method $method.est_method
@@ -27,42 +27,42 @@
 
         #if $inputs.paired_or_single == "paired":
             --left $inputs.left_input --right $inputs.right_input
-            
+
             #if $inputs.left_input.is_of_type('fasta'):
                 --seqType fa
             #else:
                 --seqType fq
             #end if
-            
+
             #if $inputs.strand.is_strand_specific:
                 --SS_lib_type $inputs.strand.library_type
             #end if
 
         #else:
             --single $inputs.input
-            
+
             #if $inputs.input.is_of_type('fasta'):
                 --seqType fa
             #else:
                 --seqType fq
             #end if
-            
+
             #if $inputs.strand.is_strand_specific:
                 --SS_lib_type $inputs.strand.library_type
             #end if
         #end if
-        
+
         --max_ins_size $inputs.paired_fragment_length
 
         ## Additional parameters.
-        #if $additional_params.gene_map.has_gene_map == "yes":
+        #if $additional_params.gene_map.has_gene_map == "no":
             --gene_trans_map $additional_params.gene_map.gene_trans_map
         #else
             --trinity_mode
         #end if
-        
+
         --prep_reference
-        
+
         --output_dir .
 
         ## CPU
@@ -106,7 +106,7 @@
                 </conditional>
             </when>
         </conditional>
-        
+
         <conditional name="method">
             <param type="select" name="est_method" label="Abundance estimation method">
                 <option value="RSEM">RSEM</option>
@@ -129,16 +129,16 @@
         <section name="additional_params" title="Additional Options" expanded="False">
             <conditional name="gene_map">
                 <param name="has_gene_map" type="select" label="Trinity assembly?" help="If the transcripts were not assembled by trinity, additional information is needed">
+                    <option value="yes">Yes</option>
                     <option value="no">No</option>
-                    <option value="yes">Yes</option>
                 </param>
-                <when value="no">
+                <when value="yes">
                 </when>
-                <when value="yes">
+                <when value="no">
                     <param format="tabular" name="gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" />
                 </when>
             </conditional>
-            
+
         </section>
     </inputs>
     <outputs>
@@ -148,7 +148,7 @@
         <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts" from_work_dir="RSEM.genes.results">
             <filter>method['est_method'] == "RSEM"</filter>
         </data>
-        
+
         <data format="tabular" name="isoforms_counts_express" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="results.xprs">
             <filter>method['est_method'] == "eXpress"</filter>
         </data>
@@ -165,7 +165,7 @@
             <param name="library_type" value="RF"/>
             <param name="est_method" value="RSEM"/>
             <param name="aln_method" value="bowtie"/>
-            <param name="has_gene_map" value="no"/>
+            <param name="has_gene_map" value="yes"/>
             <output name="isoforms_counts_rsem">
                 <assert_contents>
                     <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
@@ -187,7 +187,7 @@
             <param name="library_type" value="RF"/>
             <param name="est_method" value="RSEM"/>
             <param name="aln_method" value="bowtie2"/>
-            <param name="has_gene_map" value="no"/>
+            <param name="has_gene_map" value="yes"/>
             <output name="isoforms_counts_rsem">
                 <assert_contents>
                     <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
@@ -209,7 +209,7 @@
             <param name="library_type" value="RF"/>
             <param name="est_method" value="eXpress"/>
             <param name="aln_method" value="bowtie"/>
-            <param name="has_gene_map" value="no"/>
+            <param name="has_gene_map" value="yes"/>
             <output name="isoforms_counts_express">
                 <assert_contents>
                     <has_line_matching expression=".*&#009;TRINITY_DN2_c3_g1_i1&#009;.*" />
@@ -252,7 +252,7 @@
 .. _Trinity: http://trinityrnaseq.github.io
 ]]>
     </help>
-    
+
      <citations>
         <citation type="doi">doi:10.1038/nbt.1883</citation>
     </citations>