Mercurial > repos > rmarenco > hubarchivecreator
diff hubArchiveCreator.xml @ 26:df42241d3731 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
| author | yating-l |
|---|---|
| date | Mon, 03 Jul 2017 17:30:20 -0400 |
| parents | fcc1021bd496 |
| children | cdd33c5c8ac1 |
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--- a/hubArchiveCreator.xml Fri Jun 02 17:36:24 2017 -0400 +++ b/hubArchiveCreator.xml Mon Jul 03 17:30:20 2017 -0400 @@ -73,7 +73,8 @@ #set track_color = str($f.formatChoice.track_color) #set group_name = str($g.group_name) #set longLabel = str($f.formatChoice.longLabel) - #set extra_data_dict = {"track_color": $track_color, + #set extra_data_dict = {"database": "", + "track_color": $track_color, "group_name": $group_name, "long_label": $longLabel} @@ -109,11 +110,15 @@ #end if #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option" --bedBlastAlignments $f.formatChoice.bedChoice.BED_blast_alignment + #set database = str($f.formatChoice.bedChoice.database) + #silent extra_data_dict.update({"database": $database}) #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final, extra_data_dict) #end if #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option" --bigpsl $f.formatChoice.bedChoice.BED_blat_alignment + #set database = str($f.formatChoice.bedChoice.database) + #silent extra_data_dict.update({"database": $database}) #silent $prepare_json($f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final, extra_data_dict) #end if @@ -204,7 +209,7 @@ type="data" label="BAM File" /> - <param name="longLabel" type="text" size="80" label="Track label" /> + <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" /> <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others --> <param name="track_color" type="color" label="Track color" value="#000000"> <sanitizer> @@ -264,6 +269,12 @@ type="data" label="Bed Blast Alignments (Bed12+12) File" /> + <param name="database" type="select" label="Protein database"> + <option value="NCBI" selected="true">NCBI</option> + <option value="UniProt">UniProt</option> + <option value="FlyBase">FlyBase</option> + <option value="Others">Others</option> + </param> </when> <when value="bed_blat_alignment_option"> <param @@ -272,9 +283,13 @@ type="data" label="Bed BLAT Alignments (bigPsl) File" /> + <param name="database" type="select" label="mRNA database"> + <option value="NCBI" selected="true">NCBI</option> + <option value="Others">Others</option> + </param> </when> </conditional> - <param name="longLabel" type="text" size="30" label="Track name" /> + <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> <valid initial="string.letters,string.digits"> @@ -290,7 +305,7 @@ type="data" label="PSL File" /> - <param name="longLabel" type="text" size="30" label="Track name" /> + <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> <valid initial="string.letters,string.digits"> @@ -306,7 +321,7 @@ type="data" label="BIGWIG File" /> - <param name="longLabel" type="text" size="30" label="Track name" /> + <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> <valid initial="string.letters,string.digits"> @@ -322,7 +337,7 @@ type="data" label="BIGBED File" /> - <param name="longLabel" type="text" size="30" label="Track name" /> + <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> <valid initial="string.letters,string.digits"> @@ -338,7 +353,7 @@ type="data" label="GFF3 File" /> - <param name="longLabel" type="text" size="30" label="Track name" /> + <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> <valid initial="string.letters,string.digits"> @@ -354,7 +369,7 @@ type="data" label="GTF File" /> - <param name="longLabel" type="text" size="30" label="Track name" /> + <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> <valid initial="string.letters,string.digits">