Mercurial > repos > yating-l > jbrowsearchivecreator
diff jbrowseArchiveCreator.xml @ 13:43a700afd457 draft
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit bcb239c4045d2c47a8acad5fbd29eea03663e187
| author | yating-l |
|---|---|
| date | Tue, 19 Jun 2018 17:59:51 -0400 |
| parents | 9161beae834f |
| children | 3f9971a91096 |
line wrap: on
line diff
--- a/jbrowseArchiveCreator.xml Sat Jun 02 13:08:46 2018 -0400 +++ b/jbrowseArchiveCreator.xml Tue Jun 19 17:59:51 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.1.5"> +<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.2.1"> <description> This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin </description> @@ -81,6 +81,7 @@ #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, "group_name": $group_name, "long_label": $longLabel} @@ -88,11 +89,12 @@ #set bam_index = $f.formatChoice.BAM.metadata.bam_index ## Add Bam format specific fields - #silent $extra_data_dict.update({"index": $bam_index}) + #silent $extra_data_dict.update({"index": $bam_index, "nameIndex": str($f.formatChoice.nameIndex)}) #silent $prepare_json("Bam", $f.formatChoice.BAM, $index_track_final, $extra_data_dict) #end if #if $f.formatChoice.format_select == "bed" + #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.bedChoice.nameIndex)}) #if $f.formatChoice.bedChoice.bed_select == "bed_generic" #silent $prepare_json("Bed", $f.formatChoice.bedChoice.BED_generic, $index_track_final, $extra_data_dict) @@ -119,18 +121,22 @@ #end if #end if #if $f.formatChoice.format_select == "blastxml" - #silent $prepare_json("BlastXml", $f.formatChoice.BlastXML, $index_track_final, + #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)}) + #silent $prepare_json("BlastXml", $f.formatChoice.BlastXML, $index_track_final, extra_data_dict) #end if #if $f.formatChoice.format_select == "bigwig" + #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)}) #silent $prepare_json("BigWig", $f.formatChoice.BIGWIG, $index_track_final, $extra_data_dict) #end if #if $f.formatChoice.format_select == 'gff3' + #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)}) #silent $prepare_json("Gff3", $f.formatChoice.GFF3, $index_track_final, $extra_data_dict) #end if #if $f.formatChoice.format_select == "gtf" + #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)}) ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8 #silent $prepare_json("Gtf", $f.formatChoice.GTF, $index_track_final, $extra_data_dict) @@ -200,11 +206,12 @@ </valid> </sanitizer> </param> + <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> </when> <when value="bed"> <conditional name="bedChoice"> <param name="bed_select" type="select" label="Bed Choice"> - <option value="bed_generic">BED format</option> + <option value="bed_generic">BED Generic</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">Blast alignments (bed12+12 / bigPsl.as)</option> @@ -217,6 +224,7 @@ type="data" label="Bed File" /> + <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> </when> <when value="bed_simple_repeats_option"> <param @@ -225,6 +233,7 @@ type="data" label="Bed Simple Repeats (Bed4+12) File" /> + <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> </when> <when value="bed_splice_junctions_option"> <param @@ -233,6 +242,7 @@ type="data" label="Bed Splice Junctions (Bed12+1) File" /> + <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> </when> <when value="bed_blast_alignment_option"> <param @@ -241,6 +251,7 @@ type="data" label="Bed Blast Alignments (Bed12+12) File" /> + <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> </when> <when value="bed_blat_alignment_option"> <param @@ -249,6 +260,7 @@ type="data" label="Bed BLAT Alignments (bigPsl) File" /> + <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> </when> </conditional> <param name="longLabel" type="text" size="30" label="Track label" /> @@ -275,6 +287,7 @@ </valid> </sanitizer> </param> + <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> </when> <when value="bigwig"> <param @@ -291,6 +304,7 @@ </valid> </sanitizer> </param> + <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> </when> <when value="gff3"> <param @@ -307,6 +321,7 @@ </valid> </sanitizer> </param> + <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> </when> <when value="gtf"> <param @@ -323,7 +338,8 @@ </valid> </sanitizer> </param> - </when> + <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> + </when> </conditional> </repeat> </repeat>