Mercurial > repos > rmarenco > hubarchivecreator
diff hubArchiveCreator.xml @ 18:d786bca6a75d draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3007f4ce1d6e8ac8324970d355f028b9394e2a5f
| author | rmarenco |
|---|---|
| date | Fri, 30 Sep 2016 18:33:03 -0400 |
| parents | c02720d1afee |
| children | 40469b265ddb |
line wrap: on
line diff
--- a/hubArchiveCreator.xml Fri Sep 30 15:14:24 2016 -0400 +++ b/hubArchiveCreator.xml Fri Sep 30 18:33:03 2016 -0400 @@ -56,14 +56,32 @@ #silent data_dict.update($extra_data_dict) ## Add the ordering by taking the tool form indexes - #silent $data_dict.update({"order_index": $order_index + 1}) + #silent $data_dict.update({"order_index": $order_index}) #silent $data_parameter_dict.update({$false_path: $data_dict}) #end def + + ## Get the number of digits from tracks, to have a unique integer from group index and track index + + #set temp_max_digit = 0 + + #for $g in $group + #if len($g.format) > $temp_max_digit + #silent temp_max_digit = len($g.format) + #end if + #end for + + #set nb_digits_max_track = len(str($temp_max_digit)) + + ## END Get the number of digits + #for $i_g, $g in enumerate( $group ) #for $i, $f in enumerate( $g.format ) + ## Create the order index using index_group+1 concatenated with index_track + #set index_group_final = str($i_g + 1) + #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track) ## For each format, we have a few mandatory fields we store in a dict #set track_color = str($f.formatChoice.track_color) @@ -79,39 +97,39 @@ ## Add Bam format specific fields #silent extra_data_dict.update({"index": $bam_index}) - #silent $prepare_json($f.formatChoice.BAM, $i, extra_data_dict) + #silent $prepare_json($f.formatChoice.BAM, $index_track_final, extra_data_dict) #end if #if $f.formatChoice.format_select == "bed" #if $f.formatChoice.bedChoice.bed_select == "bed" --bed $f.formatChoice.bedChoice.BED - #silent $prepare_json($f.formatChoice.bedChoice.BED, $i, + #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final, extra_data_dict) #end if #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, $i, + #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final, extra_data_dict) #end if #end if #if $f.formatChoice.format_select == "psl" --psl $f.formatChoice.PSL - #silent $prepare_json($f.formatChoice.PSL, $i, + #silent $prepare_json($f.formatChoice.PSL, $index_track_final, extra_data_dict) #end if #if $f.formatChoice.format_select == "bigwig" --bigwig $f.formatChoice.BIGWIG - #silent $prepare_json($f.formatChoice.BIGWIG, $i, + #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final, extra_data_dict) #end if #if $f.formatChoice.format_select == "gff3" --gff3 $f.formatChoice.GFF3 - #silent $prepare_json($f.formatChoice.GFF3, $i, + #silent $prepare_json($f.formatChoice.GFF3, $index_track_final, extra_data_dict) #end if #if $f.formatChoice.format_select == "gtf" ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8 --gtf $f.formatChoice.GTF - #silent $prepare_json($f.formatChoice.GTF, $i, + #silent $prepare_json($f.formatChoice.GTF, $index_track_final, extra_data_dict) #end if #end for