# HG changeset patch
# User yating-l
# Date 1492031031 14400
# Node ID 7ddf651457df230faef24c7ed09bac88dd60c0f0
# Parent  884ee2a7168028198d8e96e5ddf054ce285f983c
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty

diff -r 884ee2a71680 -r 7ddf651457df hubArchiveCreator.xml
--- a/hubArchiveCreator.xml	Wed Apr 12 15:05:33 2017 -0400
+++ b/hubArchiveCreator.xml	Wed Apr 12 17:03:51 2017 -0400
@@ -104,6 +104,11 @@
                         #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"
                     --psl $f.formatChoice.PSL
@@ -126,11 +131,6 @@
                     #silent $prepare_json($f.formatChoice.GTF, $index_track_final,
                                              extra_data_dict)
                 #end if
-                #if $f.formatChoice.format_select == "bigpsl"
-                    --bigpsl $f.formatChoice.BIGPSL
-                    #silent $prepare_json($f.formatChoice.BIGPSL, $index_track_final,                       
-                                            extra_data_dict)
-                #end if
             #end for
         #end for
 
@@ -181,7 +181,6 @@
                         <option value="bigwig">BIGWIG</option>
                         <option value="gff3">GFF3</option>
                         <option value="gtf">GTF</option>
-                        <option value="bigpsl">BigPsl</option>
                     </param>
 
                     <when value="bam">
@@ -206,7 +205,8 @@
                                 <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="bed_blast_alignment_option">BED Blast alignments (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
@@ -241,6 +241,14 @@
                                         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>
                         <param name="track_color" type="color" label="Track color" value="#000000">
                             <sanitizer>
@@ -310,21 +318,6 @@
                             </sanitizer>
                         </param>
                     </when>
-                    <when value="bigpsl">
-                        <param 
-                                format="bigpsl"
-                                name="BIGPSL"
-                                type="data"
-                                label="bigPsl File"
-                        />
-                        <param name="track_color" type="color" label="Track color" value="#000000">
-                            <sanitizer>
-                                <valid initial="string.letters,string.digits">
-                                    <add value="#"/>
-                                </valid>
-                            </sanitizer>
-                        </param>
-                    </when>   
                 </conditional>
             </repeat>
         </repeat>