--- a/hubArchiveCreator.xml	Fri Dec 30 14:05:48 2016 -0500
+++ b/hubArchiveCreator.xml	Wed Apr 12 16:51:03 2017 -0400
@@ -1,28 +1,11 @@
-<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.0">
+<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.1">
     <description>
         This Galaxy tool permits to prepare your files to be ready for
         Assembly Hub visualization.
     </description>
 
     <requirements>
-        <!-- Conda dependencies -->
-        <requirement type="package" version="332">ucsc-bedtobigbed</requirement>
-        <requirement type="package" version="332">ucsc-fatotwobit</requirement>
-        <requirement type="package" version="332">ucsc-genepredtobed</requirement>
-        <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement>
-        <requirement type="package" version="332">ucsc-gff3togenepred</requirement>
-        <requirement type="package" version="332">ucsc-gtftogenepred</requirement>
-        <!-- TODO: Change the conda ucsc-psltobigpsl and take one > v337 because of bugs before -->
-        <!-- <requirement type="package" version="332">ucsc-psltobigpsl</requirement> -->
-        <requirement type="package" version="332">ucsc-twobitinfo</requirement>
-        <requirement type="package" version="1.3">samtools</requirement>
-        <!-- ToolShed dependencies -->
-        <requirement type="package" version="312">ucsc_tools</requirement>
-        <requirement type="package" version="0.0.1">gff3ToGenePred</requirement>
-        <requirement type="package" version="0.0.1">gtfToGenePred</requirement>
-        <requirement type="package" version="0.0.1">genePredToBed</requirement>
-        <requirement type="package" version="0.0.1">genePredToBigGenePred</requirement>
-        <requirement type="package" version="0.0.1">pslToBigPsl</requirement>
+        <requirement type="package" version="1.0">ucsc_tools_340</requirement>
         <requirement type="package" version="1.2">samtools</requirement>
     </requirements>
 
@@ -116,10 +99,15 @@
                         #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
                                                 extra_data_dict)
                     #end if
-                    #if $f.formatChoice.bedChoice.bed_select == "bigpsl_option"
-                        --bigpsl $f.formatChoice.bedChoice.bigPsl
-                        #silent $prepare_json($f.formatChoice.bedChoice.bigPsl, $index_track_final,
-                                                extra_data_dict)
+                    #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
+                        --bedBlastAlignments $f.formatChoice.bedChoice.BED_blast_alignment
+                        #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,                              
+                                             extra_data_dict)
+                    #end if
+                    #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
+                        --bigpsl $f.formatChoice.bedChoice.BED_blat_alignment
+                        #silent $prepare_json($f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,                              
+                                             extra_data_dict)
                     #end if
                 #end if
                 #if $f.formatChoice.format_select == "psl"
@@ -210,14 +198,15 @@
                                 </valid>
                             </sanitizer>
                         </param>
-                    </when>
+                    </when>     
                     <when value="bed">
                         <conditional name="bedChoice">
                             <param name="bed_select" type="select" label="Bed Choice">
                                 <option value="bed_generic" selected="true">BED Generic (bed3+)</option>
                                 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
                                 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
-                                <option value="bigpsl_option">bigPsl (bed12+12 / bigPsl.as)</option>
+                                <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option>
+                                <option value="bed_blat_alignment_option">BLAT alignments (bigPsl / bigPsl.as)</option>
                             </param>
                             <when value="bed_generic">
                                 <param
@@ -244,12 +233,20 @@
                                         label="Bed Splice Junctions (Bed12+1) File"
                                 />
                             </when>
-                            <when value="bigpsl_option">
+                            <when value="bed_blast_alignment_option">
                                 <param
                                         format="bed"
-                                        name="bigPsl"
+                                        name="BED_blast_alignment"
                                         type="data"
-                                        label="bigPsl (Bed12+12) File"
+                                        label="Bed Blast Alignments (Bed12+12) File"
+                                />
+                            </when>
+                            <when value="bed_blat_alignment_option">
+                                <param
+                                        format="bed"
+                                        name="BED_blat_alignment"
+                                        type="data"
+                                        label="Bed BLAT Alignments (bigPsl) File"
                                 />
                             </when>
                         </conditional>