Mercurial > repos > yating-l > hubarchivecreatortest
diff hubArchiveCreator.xml @ 3:fa990284327b draft default tip
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
| author | yating-l |
|---|---|
| date | Mon, 30 Oct 2017 11:58:31 -0400 |
| parents | 85195e0d4b71 |
| children |
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--- a/hubArchiveCreator.xml Fri Sep 29 14:50:50 2017 -0400 +++ b/hubArchiveCreator.xml Mon Oct 30 11:58:31 2017 -0400 @@ -123,15 +123,8 @@ #set database = str($f.formatChoice.bedChoice.database) #silent $extra_data_dict.update({"database": $database}) #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes" - #set trix_id = str($f.formatChoice.bedChoice.add_trix_index.trix_id) - #silent $extra_data_dict.update({"trix_id": $trix_id}) - #if $f.formatChoice.bedChoice.add_trix_index.index_files.index_files_type == "collection" - #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.trix_index.index_ix) - #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.trix_index.index_ixx) - #else - #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.index_ix) - #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.index_ixx) - #end if + #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ix) + #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ixx) #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index}) #end if #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final, @@ -141,15 +134,8 @@ #set database = str($f.formatChoice.bedChoice.database) #silent $extra_data_dict.update({"database": $database}) #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes" - #set trix_id = str($f.formatChoice.bedChoice.add_trix_index.trix_id) - #silent $extra_data_dict.update({"trix_id": $trix_id}) - #if $f.formatChoice.bedChoice.add_trix_index.index_files.index_files_type == "collection" - #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.trix_index.index_ix) - #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.trix_index.index_ixx) - #else - #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.index_ix) - #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.index_files.index_ixx) - #end if + #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ix) + #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ixx) #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index}) #end if #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final, @@ -166,16 +152,10 @@ #end if #if $f.formatChoice.format_select == "bigbed" #if $f.formatChoice.add_trix_index.add_trix_index_selector == "yes" - #set trix_id = str($f.formatChoice.add_trix_index.trix_id) - #silent $extra_data_dict.update({"trix_id": $trix_id}) - #if $f.formatChoice.add_trix_index.index_files.index_files_type == "collection" - #set ix_index = str($f.formatChoice.add_trix_index.index_files.trix_index.index_ix) - #set ixx_index = str($f.formatChoice.add_trix_index.index_files.trix_index.index_ixx) - #else - #set ix_index = str($f.formatChoice.add_trix_index.index_files.index_ix) - #set ixx_index = str($f.formatChoice.add_trix_index.index_files.index_ixx) - #end if - #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index}) + #set ix_index = str($f.formatChoice.add_trix_index.add_trix_file.trix_index.index_ix) + #set ixx_index = str($f.formatChoice.add_trix_index.add_trix_file.trix_index.index_ixx) + #set trix_id = str($f.formatChoice.add_trix_index.add_trix_file.trix_id) + #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index, "trix_id": $trix_id}) #end if #silent $prepare_json("BigBed", $f.formatChoice.BIGBED, $index_track_final, $extra_data_dict) @@ -377,7 +357,13 @@ label="BIGBED File" /> <expand macro="add_trix_file"> - <expand macro="specify_search_index" /> + <param + name="trix_id" + value="name" + type="text" + size="30" + label="Specify Trix identifier" + /> </expand> <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" /> <param name="track_color" type="color" label="Track color" value="#000000">