Mercurial > repos > rmarenco > hubarchivecreator
diff hubArchiveCreator.xml @ 22:7ddf651457df draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
| author | yating-l |
|---|---|
| date | Wed, 12 Apr 2017 17:03:51 -0400 |
| parents | 884ee2a71680 |
| children | 2677f1899aa8 |
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--- a/hubArchiveCreator.xml Wed Apr 12 15:05:33 2017 -0400 +++ b/hubArchiveCreator.xml Wed Apr 12 17:03:51 2017 -0400 @@ -104,6 +104,11 @@ #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 + #silent $prepare_json($f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final, + extra_data_dict) + #end if #end if #if $f.formatChoice.format_select == "psl" --psl $f.formatChoice.PSL @@ -126,11 +131,6 @@ #silent $prepare_json($f.formatChoice.GTF, $index_track_final, extra_data_dict) #end if - #if $f.formatChoice.format_select == "bigpsl" - --bigpsl $f.formatChoice.BIGPSL - #silent $prepare_json($f.formatChoice.BIGPSL, $index_track_final, - extra_data_dict) - #end if #end for #end for @@ -181,7 +181,6 @@ <option value="bigwig">BIGWIG</option> <option value="gff3">GFF3</option> <option value="gtf">GTF</option> - <option value="bigpsl">BigPsl</option> </param> <when value="bam"> @@ -206,7 +205,8 @@ <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="bed_blast_alignment_option">BED Blast alignments (bed12+12 / bigPsl.as)</option> + <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option> + <option value="bed_blat_alignment_option">BLAT alignments (bigPsl / bigPsl.as)</option> </param> <when value="bed_generic"> <param @@ -241,6 +241,14 @@ label="Bed Blast Alignments (Bed12+12) File" /> </when> + <when value="bed_blat_alignment_option"> + <param + format="bed" + name="BED_blat_alignment" + type="data" + label="Bed BLAT Alignments (bigPsl) File" + /> + </when> </conditional> <param name="track_color" type="color" label="Track color" value="#000000"> <sanitizer> @@ -310,21 +318,6 @@ </sanitizer> </param> </when> - <when value="bigpsl"> - <param - format="bigpsl" - name="BIGPSL" - type="data" - label="bigPsl File" - /> - <param name="track_color" type="color" label="Track color" value="#000000"> - <sanitizer> - <valid initial="string.letters,string.digits"> - <add value="#"/> - </valid> - </sanitizer> - </param> - </when> </conditional> </repeat> </repeat>