--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/align_and_estimate_abundance.xml	Thu Aug 27 12:23:47 2015 -0400
@@ -0,0 +1,63 @@
+<tool id='align_and_estimate_abundance' name='Align and Estimate Abundance' version='r20140717'>
+
+<description> using utility align_and_estimate_abundance.pl</description>
+
+<requirements>
+	<requirement type="package" version="r20140717">trinityrnaseq</requirement>
+	<requirement type="package" version="0.12.7">bowtie</requirement>
+	<requirement type="package" version="2.1">samtools</requirement>
+	<requirement type="package" version="1.5.1">eXpress</requirement>
+</requirements>
+
+<command> \$TRINITY_HOME/util/align_and_estimate_abundance.pl
+        --transcripts $transcripts
+        --est_method $est_method
+        --aln_method $aln_method
+        --prep_reference
+
+        ## Inputs.
+        #if str($reads.paired_or_single) == "paired":
+
+                --left $reads.left_input --right $reads.right_input
+
+                #if  $reads.left_input.ext == 'fa':
+                        --seqType fa
+                #else:
+                        --seqType fq
+                #end if
+
+                ## Additional parameters.
+                #if str($reads.optional.use_options) == "yes":
+
+                        #if str($reads.optional.library_type) != "None":
+                                --SS_lib_type $reads.optional.library_type
+                        #end if
+
+
+
+                #end if
+
+        #else:
+                --single $reads.input
+
+                #if  str($reads.input.ext) == 'fa':
+                     --seqType fa
+                #else:
+                     --seqType fq
+                #end if
+
+                ## Additional parameters.
+                #if str($reads.optional.use_option) == "yes":
+
+                        #if str($reads.additional_params.library_type) != "None":
+                                --SS_lib_type $reads.optional.library_type
+                        #end if
+
+                #end if
+        #end if
+
+## direct to output
+&gt; $align_and_estimate_abundance_log 2&gt;&amp;1
+
+</command>
+