Mercurial > repos > yating-l > hubarchivecreator
diff hubArchiveCreator.xml @ 9:d5781fe7b782 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e42ecb807fb34a8e4ddcf96944dd74d24c695352-dirty
| author | yating-l |
|---|---|
| date | Wed, 28 Dec 2016 17:33:08 -0500 |
| parents | be8fd2f24c60 |
| children | 364b8db8de17 |
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--- a/hubArchiveCreator.xml Thu Dec 22 15:32:27 2016 -0500 +++ b/hubArchiveCreator.xml Wed Dec 28 17:33:08 2016 -0500 @@ -111,6 +111,16 @@ #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final, extra_data_dict) #end if + #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option" + --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions + #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final, + extra_data_dict) + #end if + #if $f.formatChoice.bedChoice.bed_select == "bigpsl_option" + --bigpsl $f.formatChoice.bedChoice.bigPsl + #silent $prepare_json($f.formatChoice.bedChoice.bigPsl, $index_track_final, + extra_data_dict) + #end if #end if #if $f.formatChoice.format_select == "psl" --psl $f.formatChoice.PSL @@ -206,6 +216,8 @@ <param name="bed_select" type="select" label="Bed Choice"> <option value="bed_generic" selected="true">BED Generic (bed3+)</option> <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> + <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option> + <option value="bigpsl_option">bigPsl (bed12+12 / bigPsl.as)</option> </param> <when value="bed_generic"> <param @@ -224,6 +236,22 @@ label="Bed Simple Repeats (Bed4+12) File" /> </when> + <when value="bed_splice_junctions_option"> + <param + format="bed" + name="BED_splice_junctions" + type="data" + label="Bed Splice Junctions (Bed12+1) File" + /> + </when> + <when value="bigpsl_option"> + <param + format="bed" + name="bigPsl" + type="data" + label="bigPsl (Bed12+12) File" + /> + </when> </conditional> <param name="track_color" type="color" label="Track color" value="#000000"> <sanitizer> @@ -442,6 +470,7 @@ /> </output> </test> + <!-- Test with Psl --> <test>