Mercurial > repos > yating-l > jbrowse_hub
changeset 15:8627394693c6 draft
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty
| author | yating-l |
|---|---|
| date | Tue, 14 Mar 2017 14:57:39 -0400 |
| parents | 0e29c929a8ee |
| children | f2285f29a6fa |
| files | TrackHub.py jbrowse_hub.xml |
| diffstat | 2 files changed, 9 insertions(+), 6 deletions(-) [+] |
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--- 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)
--- 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" >