Mercurial > repos > iuc > jbrowse
diff jbrowse.xml @ 10:1a6d882d340d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
| author | iuc |
|---|---|
| date | Fri, 02 Dec 2016 17:58:54 -0500 |
| parents | ad4b9d7eae6a |
| children | db5fe5a3176a |
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--- a/jbrowse.xml Tue Nov 29 12:31:56 2016 -0500 +++ b/jbrowse.xml Fri Dec 02 17:58:54 2016 -0500 @@ -216,7 +216,18 @@ </blast> #else if str($track.data_format.data_format_select) == "gene_calls": <gff> - <trackType>${track.data_format.track_class}</trackType> + <trackType>${track.data_format.track_config.track_class}</trackType> + #if $track.data_format.track_config.track_class == 'JBrowse/View/Track/CanvasFeatures': + #if str($track.data_format.track_config.canvas_options.transcriptType) != "": + <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType> + #end if + #if str($track.data_format.track_config.canvas_options.subParts) != "": + <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts> + #end if + #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false": + <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs> + #end if + #end if #if $track.data_format.match_part.match_part_select: <match>${track.data_format.match_part.name}</match> #end if @@ -381,10 +392,36 @@ <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" /> - <param type="select" label="JBrowse Track Type [Advanced]" name="track_class"> - <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option> - <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option> - </param> + <conditional name="track_config"> + <param type="select" label="JBrowse Track Type [Advanced]" name="track_class"> + <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option> + <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option> + </param> + <when value="JBrowse/View/Track/CanvasFeatures"> + <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false"> + <param label="Transcript type" + name="transcriptType" + type="text" + value="" + help="If your input files represents transcripts with features not named 'mRNA', give the alternate name here (e.g. 'transcript')" + optional="True"/> + <param label="Subfeatures type" + name="subParts" + type="text" + value="" + help="If you have 'exons' but no corresponding 'CDS' features, specify here the subfeatures that should be displayed (e.g. 'exon')" + optional="True"/> + <param label="Implied UTRs" + name="impliedUTRs" + type="boolean" + checked="false" + truevalue="true" + falsevalue="false" + help="Check this your input files does not contain UTR features, but the UTR can be 'implied' from the difference between the exon and CDS boundaries"/> + </section> + </when> + <when value="JBrowse/View/Track/HTMLFeatures" /> + </conditional> <expand macro="track_styling" /> <expand macro="color_selection" /> <expand macro="track_menu" /> @@ -729,6 +766,43 @@ <param name="uglyTestingHack" value="enabled" /> <output name="output" file="menus/test.xml" lines_diff="6"/> </test> + <test> + <param name="reference_genome|genome_type_select" value="history"/> + <param name="reference_genome|genomes" value="merlin.fa"/> + <param name="gencode" value="11" /> + <param name="standalone" value="Data Directory" /> + + <repeat name="track_groups"> + <param name="category" value="With canvas config" /> + <repeat name="data_tracks"> + <conditional name="data_format"> + <param name="data_format_select" value="gene_calls"/> + <param name="annotation" value="gff3/1.gff"/> + <conditional name="match_part"> + <param name="match_part_select" value="false"/> + </conditional> + <conditional name="track_config"> + <section name="canvas_options"> + <param name="transcriptType" value="transcript"/> + <param name="subParts" value="exon"/> + <param name="impliedUTRs" value="true"/> + </section> + </conditional> + <section name="jbcolor_scale"> + <conditional name="color_score"> + <param name="color_score_select" value="none"/> + </conditional> + <conditional name="color"> + <param name="color_select" value="automatic"/> + </conditional> + </section> + </conditional> + </repeat> + </repeat> + + <param name="uglyTestingHack" value="enabled" /> + <output name="output" file="track_config/test.xml" lines_diff="6"/> + </test> </tests> <help><![CDATA[ JBrowse-in-Galaxy