--- a/align_and_estimate_abundance.xml	Mon Jan 22 11:26:51 2018 -0500
+++ b/align_and_estimate_abundance.xml	Thu Jun 14 03:11:22 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@.3">
+<tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@">
     <description>on a de novo assembly of RNA-Seq data</description>
     <macros>
         <import>macros.xml</import>
@@ -12,6 +12,12 @@
     <command detect_errors="aggressive"><![CDATA[
         ln -f -s '$transcripts' input.fa &&
 
+        #if $additional_params.gene_map.has_gene_map == "yes":
+            get_Trinity_gene_to_trans_map.pl input.fa > gene_to_trans.map &&
+        #else:
+            ln -f -s '$additional_params.gene_map.gene_trans_map' gene_to_trans.map &&
+        #end if
+
         #if $inputs.paired_or_single == "paired":
             #if $inputs.left_input.is_of_type('fasta'):
                 ln -s '$inputs.left_input' paired_left.fa &&
@@ -68,11 +74,7 @@
         #end if
 
         ## Additional parameters.
-        #if $additional_params.gene_map.has_gene_map == "no":
-            --gene_trans_map $additional_params.gene_map.gene_trans_map
-        #else
-            --trinity_mode
-        #end if
+        --gene_trans_map gene_to_trans.map
 
         --prep_reference
 
@@ -199,6 +201,7 @@
             <param name="left_input" value="reads.left.fq"/>
             <param name="right_input" value="reads.right.fq"/>
             <param name="transcripts" value="raw/Trinity.fasta"/>
+            <param name="gene_to_trans" value="raw/Trinity.map" />
             <param name="library_type" value="RF"/>
             <param name="est_method" value="RSEM"/>
             <param name="aln_method" value="bowtie"/>
@@ -221,6 +224,7 @@
             <param name="left_input" value="reads.left.fq"/>
             <param name="right_input" value="reads.right.fq"/>
             <param name="transcripts" value="raw/Trinity.fasta"/>
+            <param name="gene_to_trans" value="raw/Trinity.map" />
             <param name="library_type" value="RF"/>
             <param name="est_method" value="RSEM"/>
             <param name="aln_method" value="bowtie2"/>
@@ -243,6 +247,7 @@
             <param name="left_input" value="reads.left.fq"/>
             <param name="right_input" value="reads.right.fq"/>
             <param name="transcripts" value="raw/Trinity.fasta"/>
+            <param name="gene_to_trans" value="raw/Trinity.map" />
             <param name="library_type" value="RF"/>
             <param name="est_method" value="eXpress"/>
             <param name="aln_method" value="bowtie"/>
@@ -265,6 +270,7 @@
             <param name="left_input" value="reads.left.fq"/>
             <param name="right_input" value="reads.right.fq"/>
             <param name="transcripts" value="raw/Trinity.fasta"/>
+            <param name="gene_to_trans" value="raw/Trinity.map" />
             <param name="library_type" value="RF"/>
             <param name="est_method" value="salmon"/>
             <param name="aln_method" value="bowtie"/>
@@ -287,6 +293,7 @@
             <param name="left_input" value="reads.left.fq"/>
             <param name="right_input" value="reads.right.fq"/>
             <param name="transcripts" value="raw/Trinity.fasta"/>
+            <param name="gene_to_trans" value="raw/Trinity.map" />
             <param name="library_type" value="RF"/>
             <param name="est_method" value="kallisto"/>
             <param name="has_gene_map" value="yes"/>