Mercurial > repos > yating-l > jbrowse_hub
diff jbrowse_hub.xml @ 42:a5108e5010b4 draft
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 149c5cbda82f49f260767b5710f0c2160eebc881-dirty
| author | yating-l |
|---|---|
| date | Mon, 20 Mar 2017 12:35:33 -0400 |
| parents | 6a5f78bc0bed |
| children | b32f9f4793f8 |
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--- a/jbrowse_hub.xml Fri Mar 17 19:06:49 2017 -0400 +++ b/jbrowse_hub.xml Mon Mar 20 12:35:33 2017 -0400 @@ -35,13 +35,14 @@ #end def - + #for $g in $group #for $f in $format #set track_label = str($f.formatChoice.label) - #set extra_data_dict = {"label" : $track_label} + #set group_name = str($g.group_name) + #set extra_data_dict = {"label" : $track_label, "category" : $group_name} #if $f.formatChoice.format_select == 'bed' #set track_color = str($f.formatChoice.track_color) - #silent extra_data_dict.update({"track_color" : $track_color}) + #silent extra_data_dict.update({"color" : $track_color}) #if $f.formatChoice.bedChoice.bed_select == 'bed_simple_repeats_option' --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, extra_data_dict) @@ -56,7 +57,7 @@ #end if #if $f.formatChoice.format_select == 'gff3' #set track_color = str($f.formatChoice.track_color) - #silent extra_data_dict.update({"track_color" : $track_color}) + #silent extra_data_dict.update({"color" : $track_color}) #if $f.formatChoice.gff3Choice.gff3_select == 'gff3_transcript' --gff3_transcript $f.formatChoice.gff3Choice.GFF3_transcript #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_transcript, extra_data_dict) @@ -68,23 +69,24 @@ #if $f.formatChoice.format_select == 'blastxml' --blastxml $f.formatChoice.BlastXML #set track_color = str($f.formatChoice.track_color) - #silent extra_data_dict.update({"track_color" : $track_color}) + #silent extra_data_dict.update({"color" : $track_color}) #silent $prepare_json($f.formatChoice.BlastXML, extra_data_dict) #end if #if $f.formatChoice.format_select == 'gtf' --gtf $f.formatChoice.GTF #set track_color = str($f.formatChoice.track_color) - #silent extra_data_dict.update({"track_color" : $track_color}) + #silent extra_data_dict.update({"color" : $track_color}) #silent $prepare_json($f.formatChoice.GTF, extra_data_dict) #end if #if $f.formatChoice.format_select == 'bigwig' --bigwig $f.formatChoice.BIGWIG #set pos_color = str($f.formatChoice.pos_color) #set neg_color = str($f.formatChoice.neg_color) - #silent $extra_data_dict.update({"pos_color" : $pos_color, "neg_color" : $neg_color}) + #silent $extra_data_dict.update({"style" : {"pos_color" : $pos_color, "neg_color" : $neg_color}}) #silent $prepare_json($f.formatChoice.BIGWIG, extra_data_dict) #end if #end for + #end for #set all_data_json = json.dumps($data_parameter_dict) -j '$all_data_json' @@ -96,6 +98,8 @@ <inputs> <param name="reference" type="data" format="fasta" label="Reference Genome" /> <param name="genome_name" type="text" size="30" value="unknown" label="Genome name" /> + <repeat name="group" title="New group"> + <param type="text" name="group_name" label="Group name" value="Default group"/> <repeat name="format" title="New track"> <conditional name="formatChoice"> <param name="format_select" type="select" label="Format"> @@ -235,7 +239,8 @@ </sanitizer> </param> </when> - </conditional> + </conditional> + </repeat> </repeat> </inputs>