Mercurial > repos > yating-l > hubarchivecreator
diff hubArchiveCreator.xml @ 83:0bc486356e2a draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
| author | yating-l |
|---|---|
| date | Mon, 30 Oct 2017 12:01:23 -0400 |
| parents | 62600ac1d0f7 |
| children | cb62314a6297 |
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--- a/hubArchiveCreator.xml Wed Sep 27 17:31:19 2017 -0400 +++ b/hubArchiveCreator.xml Mon Oct 30 12:01:23 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.5.1"> +<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.5.0"> <description> This Galaxy tool permits to prepare your files to be ready for Assembly Hub visualization. @@ -122,12 +122,22 @@ #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option" #set database = str($f.formatChoice.bedChoice.database) #silent $extra_data_dict.update({"database": $database}) + #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes" + #set ix_index = str($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, $extra_data_dict) #end if #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option" #set database = str($f.formatChoice.bedChoice.database) #silent $extra_data_dict.update({"database": $database}) + #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes" + #set ix_index = str($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, $extra_data_dict) #end if @@ -141,6 +151,12 @@ $extra_data_dict) #end if #if $f.formatChoice.format_select == "bigbed" + #if $f.formatChoice.add_trix_index.add_trix_index_selector == "yes" + #set ix_index = str($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) #end if @@ -276,6 +292,7 @@ <option value="FlyBase">FlyBase</option> <option value="Others">Others</option> </param> + <expand macro="add_trix_file"/> </when> <when value="bed_blat_alignment_option"> <param @@ -288,6 +305,7 @@ <option value="NCBI" selected="true">NCBI</option> <option value="Others">Others</option> </param> + <expand macro="add_trix_file"/> </when> </conditional> <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" /> @@ -338,6 +356,15 @@ type="data" label="BIGBED File" /> + <expand macro="add_trix_file"> + <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"> <sanitizer>