# HG changeset patch
# User yating-l
# Date 1499459715 14400
# Node ID bdda7b6232d95e9c13eacedcbec8f7dfe7cbb35b
# Parent  df2a55f071fcf98169f884f61b1d268e0b4e9383
planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 8d93b27353190eb23490c9480e560d84cb60c973-dirty

diff -r df2a55f071fc -r bdda7b6232d9 jbrowse_hub.xml
--- a/jbrowse_hub.xml	Fri Jul 07 15:43:14 2017 -0400
+++ b/jbrowse_hub.xml	Fri Jul 07 16:35:15 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="1.0">
+<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="1.0.0">
     <description>
         This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse
     </description>
@@ -56,6 +56,9 @@
                 #elif $f.formatChoice.bedChoice.bed_select == 'bed_splice_junctions_option'
                     --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions
                     #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, extra_data_dict)
+                #elif $f.formatChoice.bedChoice.bed_select == 'bigpsl'
+                    --bigpsl $f.formatChoice.BigPsl
+                    #silent $prepare_json($f.formatChoice.BigPsl, extra_data_dict)
                 #end if
             #end if
             #if $f.formatChoice.format_select == 'bam'
@@ -80,10 +83,6 @@
                 --blastxml $f.formatChoice.BlastXML
                 #silent $prepare_json($f.formatChoice.BlastXML, extra_data_dict)
             #end if
-            #if $f.formatChoice.format_select == 'bigpsl'
-                --bigpsl $f.formatChoice.BigPsl
-                #silent $prepare_json($f.formatChoice.BigPsl, extra_data_dict)
-            #end if
             #if $f.formatChoice.format_select == 'gtf'
                 --gtf $f.formatChoice.GTF
                 #set track_color = str($f.formatChoice.track_color)
@@ -119,7 +118,6 @@
                         <option value="bam" selected="true">BAM</option>
                         <option value="bed">BED</option>
                         <option value="blastxml">BlastXML</option>
-                        <option value="bigpsl">BigPsl</option>
                         <option value="bigwig">BigWig</option>
                         <option value="gff3">GFF3</option>
                         <option value="gtf">GTF</option>
@@ -165,6 +163,14 @@
                                         label="Bed Splice Junctions (Bed12+1) File"
                                 />
                             </when>
+                            <when value="bigpsl">
+                            <param
+                                format="bed"
+                                name="BigPsl"
+                                type="data"
+                                label="Blat Alignments File"
+                            />
+                            </when>
                         </conditional>
                         <param name="label" type="text" size="30" value="BED file" label="Track name" />
                         <param name="track_color" type="color" label="Track color" value="#daa520">
@@ -183,15 +189,13 @@
                                 label="Blast Alignments File"
                         />
                         <param name="label" type="text" size="30" value="Blast Alignment" label="Track name" />
-                    </when>
-                    <when value="bigpsl">
-                        <param
-                                format="bigpsl"
-                                name="BigPsl"
-                                type="data"
-                                label="Blat Alignments File"
-                        />
-                        <param name="label" type="text" size="30" value="Blat Alignment" label="Track name" />
+                        <param name="track_color" type="color" label="Track color" value="#daa520">
+                            <sanitizer>
+                                <valid initial="string.letters,string.digits">
+                                    <add value="#"/>
+                                </valid>
+                            </sanitizer>
+                        </param>
                     </when>
                     <when value="bigwig">
                         <param