# HG changeset patch
# User yating-l
# Date 1489517859 14400
# Node ID 8627394693c691013cc8289e5b32f7f623e14c6d
# Parent  0e29c929a8ee74b4b0c347854b723dc799b5233d
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty

diff -r 0e29c929a8ee -r 8627394693c6 TrackHub.py
--- a/TrackHub.py	Tue Mar 14 14:43:09 2017 -0400
+++ b/TrackHub.py	Tue Mar 14 14:57:39 2017 -0400
@@ -97,6 +97,8 @@
         shutil.make_archive(self.out_path, 'zip', self.out_path)  
         shutil.rmtree(self.out_path) 
     
+    #TODO: this will list all zip files in the filedir and sub-dirs. worked in Galaxy but all list zip files in test-data when
+    #run it locally. May need modify
     def outHtml(self):
         #htmloutput = tempfile.NamedTemporaryFile(self.outfile, suffix = '.html', bufsize=0, delete=False)
         with open(self.outfile, 'w') as htmlfile:
@@ -111,6 +113,7 @@
                         relative_directory = os.path.relpath(root, filedir)
                         relative_file_path = os.path.join(relative_directory, file)
                         htmlstr += zipfiles % relative_file_path
+                        
             #htmlstr = htmlstr % zipfile
             htmlfile.write(htmlstr)
 
diff -r 0e29c929a8ee -r 8627394693c6 jbrowse_hub.xml
--- a/jbrowse_hub.xml	Tue Mar 14 14:43:09 2017 -0400
+++ b/jbrowse_hub.xml	Tue Mar 14 14:57:39 2017 -0400
@@ -28,10 +28,10 @@
                 --bam $f.formatChoice.BAM
             #end if
             #if $f.formatChoice.format_select == 'gff3_transcript'
-                --gff3_transcript $f.formatChoice.GFF3-transcript
+                --gff3_transcript $f.formatChoice.GFF3_transcript
             #end if
             #if $f.formatChoice.format_select == 'gff3_mrna'
-                --gff3_mrna $f.formatChoice.GFF3-mrna
+                --gff3_mrna $f.formatChoice.GFF3_mrna
             #end if
             #if $f.formatChoice.format_select == 'blastxml'
                 --blastxml $f.formatChoice.BlastXML
@@ -114,7 +114,7 @@
                     <when value="gff3_transcript">
                         <param
                                 format="gff3"
-                                name="GFF3-transcript"
+                                name="GFF3_transcript"
                                 type="data"
                                 label="GFF3 File"
                         />
@@ -122,7 +122,7 @@
                     <when value="gff3_mrna">
                         <param
                                 format="gff3"
-                                name="GFF3-mrna"
+                                name="GFF3_mrna"
                                 type="data"
                                 label="GFF3 File"
                         />
@@ -148,8 +148,8 @@
             <param name="output" value="hubtest" />
             <repeat name="format">
                 <conditional name="formatChoice">
-                    <param name="format_select" value="gff3"/>
-                    <param name="GFF3-transcript" value="dbia3/raw/Augustus_on_data_3__GTF_GFF.gff3" />
+                    <param name="format_select" value="gff3_transcript"/>
+                    <param name="GFF3_transcript" value="dbia3/raw/Augustus_on_data_3__GTF_GFF.gff3" />
                 </conditional>
             </repeat>
             <output name="output" file="hubtest" >