Mercurial > repos > iuc > jbrowse
diff jbrowse.xml @ 30:12d5699f92e9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
| author | iuc |
|---|---|
| date | Sat, 25 Jun 2016 15:07:08 -0400 |
| parents | 5614cf75bb24 |
| children | ce9d92980c78 |
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--- a/jbrowse.xml Thu Dec 31 11:51:40 2015 -0500 +++ b/jbrowse.xml Sat Jun 25 15:07:08 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="jbrowse" name="JBrowse" version="0.4"> +<tool id="jbrowse" name="JBrowse" version="0.5"> <description>genome browser</description> <macros> <import>macros.xml</import> @@ -7,20 +7,27 @@ <expand macro="stdio"/> <version_command>python jbrowse.py --version</version_command> <command><![CDATA[ -mkdir -p $output.files_path && + +#if $action.action_select == "create": + mkdir -p $output.files_path; +#else: + cp -R $action.update_jbrowse.extra_files_path $output.files_path; +#end if + ## Copy the XML file into the directory, mostly for debugging ## but nice if users want to reproduce locally cp $trackxml $output.files_path/galaxy.xml && ## Once that's done, we run the python script to handle the real work python $__tool_directory__/jbrowse.py -$trackxml --jbrowse \${JBROWSE_SOURCE_DIR} #if str($standalone) == "Complete": --standalone #end if ---outdir $output.files_path; + +--outdir $output.files_path +$trackxml; #if str($standalone) == "Complete": mv $output.files_path/index.html $output; @@ -65,15 +72,29 @@ <metadata> <gencode>$gencode</gencode> <genomes> - #for $genome in $genomes: + #if str($action.genomes) != "None": + #for $genome in $action.genomes: <genome>$genome</genome> #end for + #end if </genomes> + <general> + <defaultLocation>${jbgen.defaultLocation}</defaultLocation> + <trackPadding>${jbgen.trackPadding}</trackPadding> + + <shareLink>${jbgen.shareLink}</shareLink> + <aboutDescription>${jbgen.aboutDescription}</aboutDescription> + <show_tracklist>${jbgen.show_tracklist}</show_tracklist> + <show_nav>${jbgen.show_nav}</show_nav> + <show_overview>${jbgen.show_overview}</show_overview> + <show_menu>${jbgen.show_menu}</show_menu> + <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions> + </general> </metadata> <tracks> #for $tg in $track_groups: #for $track in $tg.data_tracks: - <track cat="${tg.category}" format="${track.data_format.data_format_select}"> + <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> <files> #for $dataset in $track.data_format.annotation: <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}" /> @@ -174,10 +195,18 @@ </blast> #else if str($track.data_format.data_format_select) == "gene_calls": <gff> + <trackType>${track.data_format.track_class}</trackType> #if $track.data_format.match_part.match_part_select: <match>${track.data_format.match_part.name}</match> #end if </gff> +## #else if str($track.data_format.data_format_select) == "sparql": +## <sparql> +## <url>${track.data_format.url}</url> +## <label>${track.data_format.label}</label> +## <!-- This is going to be an absolutey nightmare --> +## <query>${track.data_format.query}</query> +## </sparql> #end if </options> </track> @@ -189,11 +218,33 @@ </configfile> </configfiles> <inputs> - <param label="Fasta Sequence(s)" - name="genomes" - type="data" - format="fasta" - multiple="True"/> + <conditional name="action" label="Action"> + <param type="select" label="JBrowse-in-Galaxy Action" name="action_select"> + <option value="create">New JBrowse Instance</option> + <option value="update">Update exising JBrowse Instance</option> + </param> + <when value="create"> + <param label="Fasta Sequence(s)" + name="genomes" + type="data" + format="fasta" + multiple="True"/> + </when> + <when value="update"> + <param label="Additional Fasta Sequence(s)" + help="If sequences are selected, they will be added to the existing JBrowse instance. You should not select any sequences if you are simply updating an existing JBrowse instance which already has the required reference sequences." + name="genomes" + type="data" + format="fasta" + optional="True" + multiple="True"/> + <param label="Previous JBrowse Instance" + name="update_jbrowse" + type="data" + format="html" /> + </when> + </conditional> + <param name="standalone" label="Produce Standalone Instance" type="boolean" truevalue="Complete" falsevalue="Data Directory" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo" checked="True"/> <param label="Genetic Code" name="gencode" type="select"> @@ -231,6 +282,7 @@ <option value="blast">Blast XML</option> <option value="wiggle">BigWig XY</option> <option value="vcf">VCF SNPs</option> + <!--<option value="sparql">SPARQL</option>--> </param> <when value="blast"> <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> @@ -262,9 +314,11 @@ <expand macro="color_selection" token_scaling_lin_select="false" token_scaling_log_select="true" /> + <expand macro="track_display" /> </when> <when value="vcf"> <expand macro="input_conditional" label="SNP Track Data" format="vcf" /> + <expand macro="track_display" /> </when> <when value="gene_calls"> <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" /> @@ -284,8 +338,13 @@ </when> <when value="false" /> </conditional> + <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> <expand macro="track_styling" /> <expand macro="color_selection" /> + <expand macro="track_display" /> </when> <when value="pileup"> <expand macro="input_conditional" label="BAM Track Data" format="bam" /> @@ -295,6 +354,7 @@ name="auto_snp" truevalue="true" falsevalue="false" /> + <expand macro="track_display" /> </when> <when value="wiggle"> <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" /> @@ -328,16 +388,121 @@ </when> </conditional> <expand macro="color_selection_minmax" /> + <expand macro="track_display" /> </when> + <!-- + <when value="sparql"> + <param type="text" label="SPARQL Server URL" name="url" /> + <param type="text" label="Track Label" name="key" value="SPARQL Genes" /> + <param type="text" label="SPARQL Query" name="query" area="true" /> + <expand macro="track_display" /> + </when> + --> </conditional> </repeat> </repeat> + <expand macro="general_options" /> <param type="hidden" name="uglyTestingHack" value="" /> </inputs> <outputs> <data format="html" name="output" label="JBrowse on $on_string - $standalone"/> </outputs> + <tests> + <test> + <!-- gencode --> + <param name="genomes" value="merlin.fa"/> + <param name="gencode" value="1" /> + <param name="standalone" value="Data Directory" /> + <param name="uglyTestingHack" value="enabled" /> + <output name="output" file="gencode/test-1.xml" lines_diff="4" /> + </test> + <test> + <param name="genomes" value="merlin.fa"/> + <param name="gencode" value="11" /> + <param name="standalone" value="Data Directory" /> + <param name="uglyTestingHack" value="enabled" /> + <output name="output" file="gencode/test.xml" lines_diff="4"/> + </test> + <!-- + <test> + <param name="genomes" value="merlin.fa"/> + <param name="gencode" value="11" /> + <param name="standalone" value="Data Directory" /> + <param name="track_groups_0|category" value="Auto Coloured" /> + <param name="track_groups_0|data_tracks_0|data_format" value="gene_calls"/> + <param name="track_groups_0|data_tracks_0|annotation" value="gff3/A.gff,gff3/B.gff,gff3/C.gff,gff3/D.gff"/> + <param name="track_groups_0|data_tracks_0|match_part|match_part_select" value="false"/> + <param name="track_groups_0|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="none"/> + <param name="track_groups_0|data_tracks_0|jbcolor_scale|color|color_select" value="automatic"/> + + + <param name="track_groups_1|category" value="Ignore Scale" /> + <param name="track_groups_1|data_tracks_0|data_format" value="gene_calls"/> + <param name="track_groups_1|data_tracks_0|annotation" value="gff3/1.gff"/> + <param name="track_groups_1|data_tracks_0|match_part|match_part_select" value="false"/> + <param name="track_groups_1|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="none"/> + <param name="track_groups_1|data_tracks_0|jbcolor_scale|color_score|color|color_select" value="manual"/> + <param name="track_groups_1|data_tracks_0|jbcolor_scale|color_score|color|style_color" value="#ff00ff"/> + + <param name="track_groups_2|category" value="Scaled Colour" /> + <param name="track_groups_2|data_tracks_0|data_format" value="gene_calls"/> + <param name="track_groups_2|data_tracks_0|annotation" value="gff3/1.gff"/> + <param name="track_groups_2|data_tracks_0|match_part|match_part_select" value="false"/> + <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="score"/> + <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|score_scaling" value="linear"/> + <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> + <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> + <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|color_scheme|color_select" value="automatic"/> + <param name="track_groups_2|data_tracks_1|data_format" value="gene_calls"/> + <param name="track_groups_2|data_tracks_1|annotation" value="gff3/1.gff"/> + <param name="track_groups_2|data_tracks_1|match_part|match_part_select" value="false"/> + <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_score_select" value="score"/> + <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|score_scaling" value="linear"/> + <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> + <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> + <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_scheme|color_select" value="manual"/> + <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_scheme|style_color" value="#0000ff"/> + <param name="track_groups_2|data_tracks_2|data_format" value="gene_calls"/> + <param name="track_groups_2|data_tracks_2|annotation" value="gff3/1.gff"/> + <param name="track_groups_2|data_tracks_2|match_part|match_part_select" value="false"/> + <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|color_score_select" value="score"/> + <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scaling" value="linear"/> + <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> + <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scales|minimum" value="0"/> + <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scales|maximum" value="1000"/> + <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> + <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|color_scheme|color_select" value="automatic"/> + <param name="track_groups_2|data_tracks_3|data_format" value="gene_calls"/> + <param name="track_groups_2|data_tracks_3|annotation" value="gff3/1.gff"/> + <param name="track_groups_2|data_tracks_3|match_part|match_part_select" value="false"/> + <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_score_select" value="score"/> + <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scaling" value="linear"/> + <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> + <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scales|minimum" value="0"/> + <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scales|maximum" value="1000"/> + <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> + <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_scheme|color_select" value="manual"/> + <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_scheme|style_color" value="#ff0000"/> + + <param name="track_groups_3|category" value="Realistic" /> + <param name="track_groups_3|data_tracks_0|data_format" value="gene_calls"/> + <param name="track_groups_3|data_tracks_0|annotation" value="gff3/interpro.gff"/> + <param name="track_groups_3|data_tracks_0|match_part|match_part_select" value="false"/> + <param name="track_groups_3|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="none"/> + <param name="track_groups_3|data_tracks_0|jbcolor_scale|color|color_select" value="automatic"/> + <param name="track_groups_3|data_tracks_1|data_format" value="gene_calls"/> + <param name="track_groups_3|data_tracks_1|annotation" value="gff3/2.gff"/> + <param name="track_groups_3|data_tracks_1|match_part|match_part_select" value="true"/> + <param name="track_groups_3|data_tracks_1|match_part|name" value="cDNA_match"/> + <param name="track_groups_3|data_tracks_1|jbcolor_scale|color_score|color_score_select" value="none"/> + <param name="track_groups_3|data_tracks_1|jbcolor_scale|color|color_select" value="automatic"/> + + <param name="uglyTestingHack" value="enabled" /> + <output name="output" file="gff3/test.xml" /> + </test> + --> + </tests> <help><![CDATA[ JBrowse-in-Galaxy ================= @@ -504,7 +669,7 @@ JiG now supports both blastn and blastp datasets. JiG internally uses a blastXML to gapped GFF3 tool to convert your blastxml datasets into a -format ammenable to visualization in JBrowse. This tool is also +format amenable to visualization in JBrowse. This tool is also available separately from the IUC on the toolshed. **Minimum Gap Size** reflects how long a gap must be before it becomes a @@ -543,7 +708,7 @@ **XYPlot** BigWig tracks can be displayed as a "density" plot which is continuous -line which varies in colour, or as an "XYplot." XYplots are preferrable +line which varies in colour, or as an "XYplot." XYplots are preferable for users to visually identify specific features in a bigwig track, however density tracks are more visually compact. @@ -561,7 +726,7 @@ **autoscaling locally** instead. In the example of a region which varies from 0-50, autoscaling locally would cause the individual track's viewport to re-adjust and show just the 0-50 region. If neither of these -options are paletable, you may manually hardcode the minimum and +options are palatable, you may manually hardcode the minimum and maximums for the track to scale to. Colour Options @@ -595,101 +760,6 @@ @ATTRIBUTION@ ]]></help> - <tests> - <test> - <!-- gencode --> - <param name="genomes" value="merlin.fa"/> - <param name="gencode" value="1" /> - <param name="standalone" value="Data Directory" /> - <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="gencode/test-1.xml" lines_diff="4" /> - </test> - <test> - <param name="genomes" value="merlin.fa"/> - <param name="gencode" value="11" /> - <param name="standalone" value="Data Directory" /> - <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="gencode/test.xml" lines_diff="4"/> - </test> - <!-- - <test> - <param name="genomes" value="merlin.fa"/> - <param name="gencode" value="11" /> - <param name="standalone" value="Data Directory" /> - <param name="track_groups_0|category" value="Auto Coloured" /> - <param name="track_groups_0|data_tracks_0|data_format" value="gene_calls"/> - <param name="track_groups_0|data_tracks_0|annotation" value="gff3/A.gff,gff3/B.gff,gff3/C.gff,gff3/D.gff"/> - <param name="track_groups_0|data_tracks_0|match_part|match_part_select" value="false"/> - <param name="track_groups_0|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="none"/> - <param name="track_groups_0|data_tracks_0|jbcolor_scale|color|color_select" value="automatic"/> - - - <param name="track_groups_1|category" value="Ignore Scale" /> - <param name="track_groups_1|data_tracks_0|data_format" value="gene_calls"/> - <param name="track_groups_1|data_tracks_0|annotation" value="gff3/1.gff"/> - <param name="track_groups_1|data_tracks_0|match_part|match_part_select" value="false"/> - <param name="track_groups_1|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="none"/> - <param name="track_groups_1|data_tracks_0|jbcolor_scale|color_score|color|color_select" value="manual"/> - <param name="track_groups_1|data_tracks_0|jbcolor_scale|color_score|color|style_color" value="#ff00ff"/> - - <param name="track_groups_2|category" value="Scaled Colour" /> - <param name="track_groups_2|data_tracks_0|data_format" value="gene_calls"/> - <param name="track_groups_2|data_tracks_0|annotation" value="gff3/1.gff"/> - <param name="track_groups_2|data_tracks_0|match_part|match_part_select" value="false"/> - <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="score"/> - <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|score_scaling" value="linear"/> - <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> - <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> - <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|color_scheme|color_select" value="automatic"/> - <param name="track_groups_2|data_tracks_1|data_format" value="gene_calls"/> - <param name="track_groups_2|data_tracks_1|annotation" value="gff3/1.gff"/> - <param name="track_groups_2|data_tracks_1|match_part|match_part_select" value="false"/> - <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_score_select" value="score"/> - <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|score_scaling" value="linear"/> - <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> - <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> - <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_scheme|color_select" value="manual"/> - <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_scheme|style_color" value="#0000ff"/> - <param name="track_groups_2|data_tracks_2|data_format" value="gene_calls"/> - <param name="track_groups_2|data_tracks_2|annotation" value="gff3/1.gff"/> - <param name="track_groups_2|data_tracks_2|match_part|match_part_select" value="false"/> - <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|color_score_select" value="score"/> - <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scaling" value="linear"/> - <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> - <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scales|minimum" value="0"/> - <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scales|maximum" value="1000"/> - <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> - <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|color_scheme|color_select" value="automatic"/> - <param name="track_groups_2|data_tracks_3|data_format" value="gene_calls"/> - <param name="track_groups_2|data_tracks_3|annotation" value="gff3/1.gff"/> - <param name="track_groups_2|data_tracks_3|match_part|match_part_select" value="false"/> - <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_score_select" value="score"/> - <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scaling" value="linear"/> - <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/> - <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scales|minimum" value="0"/> - <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scales|maximum" value="1000"/> - <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/> - <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_scheme|color_select" value="manual"/> - <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_scheme|style_color" value="#ff0000"/> - - <param name="track_groups_3|category" value="Realistic" /> - <param name="track_groups_3|data_tracks_0|data_format" value="gene_calls"/> - <param name="track_groups_3|data_tracks_0|annotation" value="gff3/interpro.gff"/> - <param name="track_groups_3|data_tracks_0|match_part|match_part_select" value="false"/> - <param name="track_groups_3|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="none"/> - <param name="track_groups_3|data_tracks_0|jbcolor_scale|color|color_select" value="automatic"/> - <param name="track_groups_3|data_tracks_1|data_format" value="gene_calls"/> - <param name="track_groups_3|data_tracks_1|annotation" value="gff3/2.gff"/> - <param name="track_groups_3|data_tracks_1|match_part|match_part_select" value="true"/> - <param name="track_groups_3|data_tracks_1|match_part|name" value="cDNA_match"/> - <param name="track_groups_3|data_tracks_1|jbcolor_scale|color_score|color_score_select" value="none"/> - <param name="track_groups_3|data_tracks_1|jbcolor_scale|color|color_select" value="automatic"/> - - <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="gff3/test.xml" /> - </test> - --> - </tests> <citations> <citation type="doi">10.1101/gr.094607.109</citation> </citations>