Mercurial > repos > iuc > jbrowse
diff jbrowse.xml @ 31:2bb2e07a7a21 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
author | iuc |
---|---|
date | Mon, 15 Apr 2019 10:31:26 -0400 |
parents | ca2def38369c |
children | 0ae74c70b267 |
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--- a/jbrowse.xml Thu Apr 11 09:35:00 2019 -0400 +++ b/jbrowse.xml Mon Apr 15 10:31:26 2019 -0400 @@ -210,6 +210,15 @@ #end for </menus> #end if + #if str($track.data_format.data_format_select) in ["gene_calls", "pileup", "blast", "wiggle", "vcf"]: + <custom_config> + #for $custom_option in $track.data_format.jb_custom_config.option: + <${custom_option.opt_key}> + <${custom_option.opt_value.val_type}>${$custom_option.opt_value.val}</${custom_option.opt_value.val_type}> + </${custom_option.opt_key}> + #end for + </custom_config> + #end if #if str($track.data_format.data_format_select) == "wiggle": <wiggle> @@ -318,7 +327,8 @@ BlastView="${plugins.BlastView}" theme="" /> -</root>]]></configfile> +</root> +]]></configfile> </configfiles> <inputs> <conditional name="reference_genome"> @@ -431,11 +441,13 @@ <expand macro="color_selection" token_scaling_lin_select="false" token_scaling_log_select="true" /> + <expand macro="track_custom_config" /> <expand macro="track_menu" /> <expand macro="track_display" /> </when> <when value="vcf"> <expand macro="input_conditional" label="SNP Track Data" format="vcf" /> + <expand macro="track_custom_config" /> <expand macro="track_display" /> </when> <when value="gene_calls"> @@ -487,6 +499,7 @@ description="note,description" height="10px"/> <expand macro="color_selection" /> + <expand macro="track_custom_config" /> <expand macro="track_menu" /> <expand macro="track_display" /> </when> @@ -503,6 +516,7 @@ type="integer" help="Maximum size in bytes of BAM chunks that the browser will try to deal with. When this is exceeded, most tracks will display 'Too much data' message." value="5000000" /> + <expand macro="track_custom_config" /> <expand macro="track_display" /> </when> <when value="wiggle"> @@ -545,6 +559,7 @@ help="MultiBigWig is a plugin to group multiple big-wig tracks in a more aesthetically pleasing format and to show data in a higher density display." /> <expand macro="color_selection_minmax" /> + <expand macro="track_custom_config" /> <expand macro="track_display" /> </when> <when value="rest"> @@ -642,7 +657,7 @@ <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="14"/> + <output name="output" file="gencode/test-1.xml" lines_diff="16"/> </test> <test> <param name="reference_genome|genome_type_select" value="history"/> @@ -650,7 +665,7 @@ <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="14"/> + <output name="output" file="gencode/test.xml" lines_diff="16"/> </test> <test> <param name="reference_genome|genome_type_select" value="history"/> @@ -846,7 +861,7 @@ </repeat> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="gff3/test.xml" lines_diff="256" /> + <output name="output" file="gff3/test.xml" lines_diff="170" /> </test> <test> <param name="reference_genome|genome_type_select" value="history"/> @@ -909,7 +924,7 @@ </repeat> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="menus/test.xml" lines_diff="24"/> + <output name="output" file="menus/test.xml" lines_diff="44"/> </test> <test> <param name="reference_genome|genome_type_select" value="history"/> @@ -927,6 +942,7 @@ <param name="match_part_select" value="false"/> </conditional> <conditional name="track_config"> + <param name="track_class" value="JBrowse/View/Track/CanvasFeatures"/> <section name="canvas_options"> <param name="transcriptType" value="transcript"/> <param name="subParts" value="exon"/> @@ -946,7 +962,59 @@ </repeat> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="track_config/test.xml" lines_diff="26"/> + <output name="output" file="track_config/test.xml" lines_diff="30"/> + </test> + <test> + <param name="reference_genome|genome_type_select" value="history"/> + <param name="reference_genome|genome" value="merlin.fa"/> + <param name="gencode" value="11" /> + <param name="standalone" value="Data Directory" /> + + <repeat name="track_groups"> + <param name="category" value="With custom track 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> + <section name="jb_custom_config"> + <repeat name="option"> + <param name="opt_key" value="displayMode"/> + <conditional name="opt_value"> + <param name="val_type" value="text"/> + <param name="val" value="collapsed"/> + </conditional> + </repeat> + <repeat name="option"> + <param name="opt_key" value="histograms.height"/> + <conditional name="opt_value"> + <param name="val_type" value="integer"/> + <param name="val" value="150"/> + </conditional> + </repeat> + <repeat name="option"> + <param name="opt_key" value="maxFeatureScreenDensity"/> + <conditional name="opt_value"> + <param name="val_type" value="float"/> + <param name="val" value="0.1"/> + </conditional> + </repeat> + <repeat name="option"> + <param name="opt_key" value="style.strandArrow"/> + <conditional name="opt_value"> + <param name="val_type" value="boolean"/> + <param name="val" value="false"/> + </conditional> + </repeat> + </section> + </conditional> + </repeat> + </repeat> + + <param name="uglyTestingHack" value="enabled" /> + <output name="output" file="custom_config/test.xml" lines_diff="30"/> </test> <test> <param name="reference_genome|genome_type_select" value="history"/> @@ -965,7 +1033,7 @@ </repeat> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="bam/test.xml" lines_diff="48"/> + <output name="output" file="bam/test.xml" lines_diff="42"/> </test> <test> @@ -975,7 +1043,7 @@ <param name="gencode" value="1" /> <param name="standalone" value="Data Directory" /> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="gencode/test-data_table.xml" lines_diff="6" /> + <output name="output" file="gencode/test-data_table.xml" lines_diff="4" /> </test> <test> @@ -1022,7 +1090,7 @@ </repeat> <param name="uglyTestingHack" value="enabled" /> - <output name="output" file="endpoints/test.xml" lines_diff="48"/> + <output name="output" file="endpoints/test.xml" lines_diff="16"/> </test> </tests> <help><![CDATA[