annotateviz: annotateviz.xml annotate

annotate annotateviz.xml @ 1:ce990f818362 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty

author	eduardo
date	Sat, 17 Jun 2017 13:45:05 -0400
parents	7537482eed36
children	31e855c95936

rev	line source
0 7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	1 <tool id="annotateviz" name="AnnotateViz" version="0.1">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	2 <description>Annotation tool for transcriptomes</description>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	3 <macros>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	4 <import>macros.xml</import>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	5 </macros>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	6 <expand macro="requirements"/>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	7 <expand macro="stdio"/>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	8 <command><![CDATA[
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	9 mkdir -p $output.files_path &&
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	10 ## Once that's done, we run the python script to handle the real work
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	11 python $__tool_directory__/jbrowse.py
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	12 --jbrowse \${JBROWSE_SOURCE_DIR}
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	13 --standalone
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	14 --outdir $output.files_path
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	15 $trackxml &&
1 ce990f818362 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: 0 diff changeset	16 ## $output.files_path/index.html $output;
ce990f818362 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: 0 diff changeset	17 python $__tool_directory__/annotateviz.py $db > $__tool_directory__/trans.json &&
ce990f818362 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: 0 diff changeset	18 sed "s@input_db@${__app__.security.encode_id($db.id)}@" $__tool_directory__/static/trinotateviz.html > $output &&
ce990f818362 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: 0 diff changeset	19 cp $__tool_directory__/static/js/gff_app.js ${output.files_path} &&
ce990f818362 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: 0 diff changeset	20 cp $__tool_directory__/static/css/main.css ${output.files_path} &&
ce990f818362 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: 0 diff changeset	21 cp $__tool_directory__/static/trans.json ${output.files_path};
0 7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	22
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	23 ]]></command>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	24 <configfiles>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	25 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	26 <root>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	27 <metadata>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	28 <gencode>1</gencode>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	29 <genomes>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	30 <genome>$genome</genome>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	31 </genomes>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	32 <general>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	33 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	34 <trackPadding>${jbgen.trackPadding}</trackPadding>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	35
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	36 <shareLink>${jbgen.shareLink}</shareLink>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	37 <aboutDescription>${jbgen.aboutDescription}</aboutDescription>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	38 <show_tracklist>${jbgen.show_tracklist}</show_tracklist>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	39 <show_nav>${jbgen.show_nav}</show_nav>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	40 <show_overview>${jbgen.show_overview}</show_overview>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	41 <show_menu>${jbgen.show_menu}</show_menu>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	42 <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	43 </general>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	44 </metadata>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	45 <tracks>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	46 #for $tg in $track_groups:
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	47 #for $track in $tg.data_tracks:
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	48 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	49 <files>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	50 #for $dataset in $track.data_format.annotation:
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	51 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	52 #end for
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	53 </files>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	54 <options>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	55 #if str($track.data_format.data_format_select) == "gene_calls" or str($track.data_format.data_format_select) == "blast":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	56 <style>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	57 <className>${track.data_format.jbstyle.style_classname}</className>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	58 <description>${track.data_format.jbstyle.style_description}</description>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	59 <label>${track.data_format.jbstyle.style_label}</label>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	60 <height>${track.data_format.jbstyle.style_height}</height>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	61 </style>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	62 <scaling>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	63 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	64 <method>ignore</method>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	65 <scheme>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	66 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	67 <color>__auto__</color>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	68 #else
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	69 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	70 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	71 </scheme>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	72 #else
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	73 <method>score</method>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	74 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	75 <scales>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	76 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	77 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	78 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	79 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	80 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	81 </scales>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	82 <scheme>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	83 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	84 ## auto_color
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	85 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	86 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	87 <color>__auto__</color>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	88 #else
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	89 <color>${track.data_format.jbcolor_scale.color_score.color_scheme.color.style_color}</color>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	90 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	91 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	92 </scheme>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	93 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	94 </scaling>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	95 <menus>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	96 #for $menu_item in $track.data_format.jbmenu.track_menu:
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	97 <menu>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	98 <action>${menu_item.menu_action}</action>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	99 #if str($menu_item.menu_label) != "":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	100 <label>${menu_item.menu_label}</label>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	101 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	102 #if str($menu_item.menu_title) != "":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	103 <title>${menu_item.menu_title}</title>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	104 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	105 #if str($menu_item.menu_url) != "":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	106 <url>${menu_item.menu_url.replace("&", "&").replace("\"", """)}</url>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	107 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	108 #if str($menu_item.menu_icon) != "":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	109 <iconClass>${menu_item.menu_icon}</iconClass>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	110 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	111 </menu>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	112 #end for
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	113 </menus>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	114 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	115 #if str($track.data_format.data_format_select) == "wiggle":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	116 <wiggle>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	117 <type>${track.data_format.xyplot}</type>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	118 <variance_band>${track.data_format.var_band}</variance_band>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	119 #if str($track.data_format.scaling.scale_select) == "auto_local":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	120 <autoscale>local</autoscale>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	121 #else if str($track.data_format.scaling.scale_select) == "auto_global":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	122 <autoscale>global</autoscale>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	123 #else:
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	124 <min>${track.data_format.scaling.minimum}</min>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	125 <max>${track.data_format.scaling.maximum}</max>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	126 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	127 ## Wiggle tracks need special color config
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	128 #if str($track.data_format.jbcolor.color.color_select) != "automatic":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	129 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	130 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	131 #else:
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	132 <color_pos>__auto__</color_pos>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	133 <color_neg>__auto__</color_neg>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	134 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	135 ## Bicolor pivot config
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	136 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	137 <bicolor_pivot>zero</bicolor_pivot>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	138 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	139 <bicolor_pivot>mean</bicolor_pivot>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	140 #else:
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	141 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	142 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	143 </wiggle>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	144 #else if str($track.data_format.data_format_select) == "pileup":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	145 <pileup>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	146 <auto_snp>${track.data_format.auto_snp}</auto_snp>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	147 <bam_indices>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	148 #for $dataset in $track.data_format.annotation:
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	149 <bam_index>${dataset.metadata.bam_index}</bam_index>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	150 #end for
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	151 </bam_indices>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	152 </pileup>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	153 #else if str($track.data_format.data_format_select) == "blast":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	154 <blast>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	155 #if str($track.data_format.blast_parent) != "":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	156 <parent>${track.data_format.blast_parent}</parent>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	157 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	158 <protein>${track.data_format.is_protein}</protein>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	159 <min_gap>${track.data_format.min_gap}</min_gap>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	160 <index>${track.data_format.index}</index>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	161 </blast>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	162 #else if str($track.data_format.data_format_select) == "gene_calls":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	163 <gff>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	164 <trackType>${track.data_format.track_config.track_class}</trackType>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	165 #if $track.data_format.track_config.track_class == 'JBrowse/View/Track/CanvasFeatures':
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	166 #if str($track.data_format.track_config.canvas_options.transcriptType) != "":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	167 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	168 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	169 #if str($track.data_format.track_config.canvas_options.subParts) != "":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	170 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	171 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	172 #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	173 <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	174 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	175 #else if $track.data_format.track_config.track_class == 'JBrowse/View/Track/HTMLFeatures':
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	176 #if str($track.data_format.track_config.html_options.transcriptType) != "":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	177 <transcriptType>${track.data_format.track_config.html_options.transcriptType}</transcriptType>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	178 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	179 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	180 #if $track.data_format.match_part.match_part_select:
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	181 <match>${track.data_format.match_part.name}</match>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	182 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	183 <index>${track.data_format.index}</index>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	184 </gff>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	185 ## #else if str($track.data_format.data_format_select) == "sparql":
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	186 ## <sparql>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	187 ## <url>${track.data_format.url}</url>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	188 ## <label>${track.data_format.label}</label>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	189 ## <!-- This is going to be an absolutey nightmare -->
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	190 ## <query>${track.data_format.query}</query>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	191 ## </sparql>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	192 #end if
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	193 </options>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	194 </track>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	195 #end for
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	196 #end for
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	197 </tracks>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	198 </root>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	199 ]]></configfile>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	200 </configfiles>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	201 <inputs>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	202 <param name="db" type="data" format="sqlite" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	203 <param name="genome" type="data" format="fasta" optional="false" label="Peptide predictions" help="Predicted peptides in fasta format" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	204 <repeat name="track_groups" title="Track Group">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	205 <param label="Track Category"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	206 name="category"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	207 type="text"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	208 value="Default"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	209 help="Organise your tracks into Categories for a nicer end-user experience" optional="False"/>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	210 <repeat name="data_tracks" title="Annotation Track">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	211 <conditional name="data_format">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	212 <param type="select" label="Track Type" name="data_format_select">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	213 <option value="gene_calls">GFF/GFF3/BED/GBK Features</option>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	214 <option value="pileup">BAM Pileups</option>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	215 <option value="blast">Blast XML</option>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	216 <option value="wiggle">BigWig XY</option>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	217 <option value="vcf">VCF SNPs</option>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	218 <!--<option value="sparql">SPARQL</option>-->
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	219 </param>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	220 <when value="blast">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	221 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	222
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	223 <param label="Features used in Blast Search"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	224 help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this."
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	225 format="gff3"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	226 name="blast_parent"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	227 optional="true"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	228 type="data"/>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	229
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	230 <param label="Minimum Gap Size"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	231 help="before a new match_part feature is created"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	232 name="min_gap"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	233 type="integer"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	234 value="10"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	235 min="2" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	236 <param label="Is this a protein blast search?"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	237 type="boolean"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	238 name="is_protein"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	239 truevalue="true"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	240 falsevalue="false" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	241
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	242 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	243
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	244 <expand macro="track_styling"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	245 classname="feature"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	246 label="description"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	247 description="Hit_titles"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	248 height="600px"/>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	249 <expand macro="color_selection"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	250 token_scaling_lin_select="false"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	251 token_scaling_log_select="true" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	252 <expand macro="track_menu" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	253 <expand macro="track_display" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	254 </when>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	255 <when value="vcf">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	256 <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	257 <expand macro="track_display" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	258 </when>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	259 <when value="gene_calls">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	260 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	261 <conditional name="match_part">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	262 <param label="This is match/match_part data"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	263 type="boolean"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	264 name="match_part_select"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	265 truevalue="true"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	266 falsevalue="false" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	267 <when value="true">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	268 <param label="Match Part Feature Type"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	269 name="name"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	270 type="text"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	271 value="match"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	272 help="Match_parts have several options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	273 optional="False"/>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	274 </when>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	275 <when value="false" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	276 </conditional>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	277
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	278 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	279
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	280 <conditional name="track_config">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	281 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	282 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	283 <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	284 </param>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	285 <when value="JBrowse/View/Track/CanvasFeatures">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	286 <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	287 <param label="Transcript type"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	288 name="transcriptType"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	289 type="text"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	290 value=""
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	291 help="If your input files represents transcripts with features not named 'mRNA', give the alternate name here (e.g. 'transcript')"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	292 optional="True"/>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	293 <param label="Subfeatures type"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	294 name="subParts"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	295 type="text"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	296 value=""
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	297 help="If you have 'exons' but no corresponding 'CDS' features, specify here the subfeatures that should be displayed (e.g. 'exon')"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	298 optional="True"/>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	299 <param label="Implied UTRs"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	300 name="impliedUTRs"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	301 type="boolean"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	302 checked="false"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	303 truevalue="true"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	304 falsevalue="false"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	305 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"/>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	306 </section>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	307 </when>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	308 <when value="JBrowse/View/Track/HTMLFeatures">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	309 <section name="html_options" title="HTMLFeatures Options [Advanced]" expanded="false">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	310 <param label="Transcript type"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	311 name="transcriptType"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	312 type="text"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	313 value=""
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	314 help="If your input files represents transcripts, give the name of the corresponding features here (e.g. 'mRNA' or 'transcript')"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	315 optional="True"/>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	316 </section>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	317 </when>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	318 </conditional>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	319 <expand macro="track_styling" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	320 <expand macro="color_selection" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	321 <expand macro="track_menu" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	322 <expand macro="track_display" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	323 </when>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	324 <when value="pileup">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	325 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	326 <param label="Autogenerate SNP Track"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	327 help="Not recommended for deep coverage BAM files"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	328 type="boolean"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	329 name="auto_snp"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	330 truevalue="true"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	331 falsevalue="false" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	332 <expand macro="track_display" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	333 </when>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	334 <when value="wiggle">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	335 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	336
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	337 <param label="Use XYPlot"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	338 help="instead of continuous colored band"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	339 type="boolean"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	340 name="xyplot"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	341 truevalue="JBrowse/View/Track/Wiggle/XYPlot"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	342 falsevalue="JBrowse/View/Track/Wiggle/Density" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	343 <param label="Show variance band"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	344 help="Only for XYPlots"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	345 type="boolean"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	346 name="var_band"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	347 truevalue="true"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	348 falsevalue="false" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	349
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	350 <conditional name="scaling">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	351 <param type="select" label="Track Scaling" name="scale_select">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	352 <option value="auto_local">Autoscale (local)</option>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	353 <option value="auto_global" selected="true">Autoscale (global)</option>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	354 <option value="fixed">Specify Min/Max</option>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	355 </param>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	356 <when value="auto_local"></when>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	357 <when value="auto_global"></when>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	358 <when value="fixed">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	359 <param label="Track minimum" name="minimum"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	360 type="integer" value="0" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	361 <param label="Track maximum" name="maximum"
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	362 type="integer" value="100" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	363 </when>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	364 </conditional>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	365 <expand macro="color_selection_minmax" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	366 <expand macro="track_display" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	367 </when>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	368 <!--
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	369 <when value="sparql">
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	370 <param type="text" label="SPARQL Server URL" name="url" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	371 <param type="text" label="Track Label" name="key" value="SPARQL Genes" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	372 <param type="text" label="SPARQL Query" name="query" area="true" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	373 <expand macro="track_display" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	374 </when>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	375 -->
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	376 </conditional>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	377 </repeat>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	378 </repeat>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	379
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	380 <expand macro="general_options" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	381 <param type="hidden" name="uglyTestingHack" value="" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	382 </inputs>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	383 <outputs>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	384 <data format="html" name="output" label="Annotateviz $on_string "/>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	385
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	386 </outputs>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	387 <tests>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	388 <test>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	389 <param name="db" value="Trinotate_no_uniprot.sqlite" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	390 <output name="output" file="trinotateviz.html" lines_diff="2" />
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	391 </test>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	392 </tests>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	393 <help><![CDATA[
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	394
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	395
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	396
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	397 @ATTRIBUTION@
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	398 ]]></help>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	399 <expand macro="citations"/>
7537482eed36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty eduardo parents: diff changeset	400 </tool>

Mercurial > repos > eduardo > annotateviz

annotate annotateviz.xml @ 1:ce990f818362 draft