pygenometracks: pyGenomeTracks.xml annotate

annotate pyGenomeTracks.xml @ 8:4ac4e7083b7e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"

author	iuc
date	Tue, 21 Jul 2020 03:32:48 -0400
parents	326a3db8d9d1
children	2824d77cd8f8

rev	line source
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1 <tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@">
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2 <description>plot genomic data tracks</description>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	3 <macros>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	4 <token name="@BINARY@">pyGenomeTracks</token>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	5 <import>macros.xml</import>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	6 </macros>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	7 <expand macro="requirements" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	8 <command detect_errors="exit_code">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	9 <![CDATA[
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	10 ## First symlink data of hic to have the good extension
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	11 #for $counter, $track in enumerate($tracks):
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	12 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	13 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	14 #set ext = $data_matrix.extension
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	15 ln -s $data_matrix ${counter}_${counter_matrix}.$ext &&
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	16 #end for
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	17 #end if
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	18 #end for
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	19
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	20
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	21 sed '/^$/d' '$tracks_config' &&
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	22 @BINARY@
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	23 --tracks '$tracks_config'
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	24 #if $region and $region is not None:
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	25 --region '$region'
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	26 #end if
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	27 #if $global_args.title is not None:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	28 --title '$global_args.title'
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	29 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	30 --fontSize $global_args.fontsize
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	31 --dpi $global_args.dpi
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	32 --trackLabelFraction $global_args.trackLabelFraction
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	33 --trackLabelHAlign $global_args.trackLabelHAlign
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	34 --outFileName plot.$image_file_format
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	35 $global_args.decreasingXAxis
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	36 && mv plot.$image_file_format plot
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	37 ]]>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	38 </command>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	39 <configfiles>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	40 <configfile name="tracks_config">
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	41 ## Each track:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	42 #for $counter, $track in enumerate($tracks):
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	43 ## Hi-C Track
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	44 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	45 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	46 [hic_section_${counter}_${counter_matrix}]
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	47 #set ext = $data_matrix.extension
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	48 file = ${counter}_${counter_matrix}.$ext
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	49 file_type = hic_matrix
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	50 #if $track.track_file_style_conditional.title:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	51 title = $track.track_file_style_conditional.title
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	52 #else:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	53 title = $data_matrix.name
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	54 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	55 #if $track.track_file_style_conditional.depth:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	56 depth = $track.track_file_style_conditional.depth
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	57 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	58 #if $track.track_file_style_conditional.colormap:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	59 colormap = $track.track_file_style_conditional.colormap
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	60 #end if
6 5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	61 #if $track.track_file_style_conditional.min_value != "":
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	62 min_value = $track.track_file_style_conditional.min_value
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	63 #end if
6 5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	64 #if $track.track_file_style_conditional.max_value != "":
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	65 max_value = $track.track_file_style_conditional.max_value
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	66 #end if
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	67 transform = $track.track_file_style_conditional.transform
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	68 #if $track.track_file_style_conditional.height_matrix != "":
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	69 height = $track.track_file_style_conditional.height_matrix
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	70 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	71 #if $track.track_file_style_conditional.show_masked_bins:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	72 show_masked_bins = $track.track_file_style_conditional.show_masked_bins
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	73 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	74 #if $track.track_file_style_conditional.invert_orientation:
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	75 orientation = inverted
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	76 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	77 #if $track.track_file_style_conditional.scale_factor:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	78 scale_factor = $track.track_file_style_conditional.scale_factor
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	79 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	80 rasterize = $track.track_file_style_conditional.rasterize
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	81 ## If a boundary file is given a new section needs to be written:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	82 #if str($track.track_file_style_conditional.boundaries_file) != "None":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	83 #if len($track.track_file_style_conditional.boundaries_file)>$counter_matrix:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	84 #set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix]
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	85 #else:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	86 #set boundary_file = $track.track_file_style_conditional.boundaries_file[0]
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	87 #end if
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	88 [tads_${counter}_${counter_matrix}]
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	89 file = $boundary_file
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	90 file_type = domains
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	91 border_color = black
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	92 color = none
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	93 overlay_previous = share-y
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	94 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	95 ## If spacer is asked a new section is created:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	96 #if $track.track_file_style_conditional.spacer_height != "":
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	97 [spacer]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	98 height = $track.track_file_style_conditional.spacer_height
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	99 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	100 #end for
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	101 #end if
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	102
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	103 ## Chrom_state track
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	104 #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	105 #for $data_bed in $track.track_file_style_conditional.track_input_bed:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	106 [chrom states_$counter]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	107 file = $data_bed
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	108 #if $track.track_file_style_conditional.title:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	109 title = $track.track_file_style_conditional.title
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	110 #else:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	111 title = $data_bed.name
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	112 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	113 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	114 color = bed_rgb
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	115 #elif $track.track_file_style_conditional.color_bed.color:
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	116 color = $track.track_file_style_conditional.color_bed.color
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	117 #end if
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	118 #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually':
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	119 border_color = $track.track_file_style_conditional.border_color_bed.color
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	120 #else
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	121 border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	122 #end if
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	123 display = collapsed
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	124 #if $track.track_file_style_conditional.height_chrom:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	125 height = $track.track_file_style_conditional.height_chrom
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	126 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	127 line_width = $track.track_file_style_conditional.line_width
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	128 file_type = bed
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	129 ## If spacer is asked a new section is created:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	130 #if $track.track_file_style_conditional.spacer_height != "":
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	131 [spacer]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	132 height = $track.track_file_style_conditional.spacer_height
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	133 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	134 #end for
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	135 #end if
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	136
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	137 ## Gene/gtf track
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	138 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	139 #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed):
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	140 [genes_${counter}_${counter_bed}]
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	141 #set ext = $data_bed.extension
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	142 file = $data_bed
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	143 #if $ext == 'gtf':
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	144 prefered_name = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.prefered_name
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	145 merge_transcripts = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	146 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	147 #if $track.track_file_style_conditional.title:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	148 title = $track.track_file_style_conditional.title
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	149 #elif $track.track_file_style_conditional.overlay_select == 'no':
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	150 title = $data_bed.name
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	151 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	152 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	153 color = bed_rgb
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	154 #elif $track.track_file_style_conditional.color_bed.color:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	155 color = $track.track_file_style_conditional.color_bed.color
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	156 #end if
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	157 #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually':
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	158 border_color = $track.track_file_style_conditional.border_color_bed.color
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	159 #else
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	160 border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	161 #end if
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	162 style = $track.track_file_style_conditional.bed_style.bed_style_select
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	163 #if $track.track_file_style_conditional.bed_style.bed_style_select == 'UCSC':
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	164 arrow_interval = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_interval
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	165 #else:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	166 height_utr = $track.track_file_style_conditional.bed_style.bed_advanced.height_utr
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	167 #if $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'manually':
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	168 color_utr = $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	169 #elif $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'bed_rgb':
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	170 color_utr = bed_rgb
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	171 #else:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	172 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	173 color_utr = bed_rgb
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	174 #else:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	175 color_utr = $track.track_file_style_conditional.color_bed.color
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	176 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	177 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	178 #if $track.track_file_style_conditional.bed_style.bed_style_select == 'tssarrow' and $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length != '':
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	179 arrow_length = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	180 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	181 #if $track.track_file_style_conditional.bed_style.bed_style_select == 'flybase':
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	182 arrowhead_included = $track.track_file_style_conditional.bed_style.arrowhead_included
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	183 #end if
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	184 #end if
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	185 display = $track.track_file_style_conditional.display
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	186 #if $track.track_file_style_conditional.height_bed:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	187 height = $track.track_file_style_conditional.height_bed
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	188 #end if
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	189 labels = $track.track_file_style_conditional.labels.plot_labels
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	190 #if $track.track_file_style_conditional.labels.plot_labels == 'true':
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	191 all_labels_inside = $track.track_file_style_conditional.labels.all_labels_inside
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	192 labels_in_margin = $track.track_file_style_conditional.labels.labels_in_margin
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	193 #end if
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	194 file_type = $ext
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	195 #if $track.track_file_style_conditional.fontsize:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	196 fontsize = $track.track_file_style_conditional.fontsize
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	197 #end if
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	198 #if $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	199 gene_rows = $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	200 #end if
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	201 global_max_row = $track.track_file_style_conditional.bed_style.bed_advanced.global_max_row
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	202 max_labels = $track.track_file_style_conditional.bed_style.bed_advanced.max_labels
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	203 line_width = $track.track_file_style_conditional.bed_style.bed_advanced.line_width
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	204 #if $track.track_file_style_conditional.invert_orientation:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	205 orientation = inverted
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	206 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	207 overlay_previous = $track.track_file_style_conditional.overlay_select
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	208 ## If spacer is asked a new section is created:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	209 #if $track.track_file_style_conditional.spacer_height != "":
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	210 [spacer]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	211 height = $track.track_file_style_conditional.spacer_height
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	212 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	213 #end for
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	214 #end if
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	215
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	216 ## Link
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	217 #if $track.track_file_style_conditional.track_file_style_selector == "link_track_option":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	218 [links_$counter]
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	219 file = $track.track_file_style_conditional.track_input_link
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	220 #if $track.track_file_style_conditional.title:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	221 title = $track.track_file_style_conditional.title
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	222 #elif $track.track_file_style_conditional.overlay_select == 'no':
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	223 title = $track.track_file_style_conditional.track_input_link.name
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	224 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	225 #if $track.track_file_style_conditional.height:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	226 height = $track.track_file_style_conditional.height
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	227 #end if
6 5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	228 #if $track.track_file_style_conditional.min_value != "":
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	229 min_value = $track.track_file_style_conditional.min_value
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	230 #end if
6 5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	231 #if $track.track_file_style_conditional.max_value != "":
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	232 max_value = $track.track_file_style_conditional.max_value
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	233 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	234 color = $track.track_file_style_conditional.color_link.color
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	235 alpha = $track.track_file_style_conditional.alpha
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	236 line_width = $track.track_file_style_conditional.line_width
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	237 line_style = $track.track_file_style_conditional.line_style
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	238 links_type = $track.track_file_style_conditional.links_type
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	239 compact_arcs_level = $track.track_file_style_conditional.compact_arcs_level
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	240 #if $track.track_file_style_conditional.ylim != "":
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	241 ylim = $track.track_file_style_conditional.ylim
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	242 #end if
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	243 use_middle = $track.track_file_style_conditional.use_middle
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	244 #if $track.track_file_style_conditional.invert_orientation:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	245 orientation = inverted
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	246 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	247 overlay_previous = $track.track_file_style_conditional.overlay_select
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	248 file_type = links
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	249 ## If spacer is asked a new section is created:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	250 #if $track.track_file_style_conditional.spacer_height != "":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	251 [spacer]
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	252 height = $track.track_file_style_conditional.spacer_height
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	253 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	254 #end if
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	255
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	256 ## Narrow peak
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	257 #if $track.track_file_style_conditional.track_file_style_selector == "narrow_peak_track_option":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	258 #for $counter_narrow_peak, $data_narrow_peak in enumerate($track.track_file_style_conditional.track_input_narrow_peak):
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	259 [narrow_peak_${counter}_${counter_narrow_peak}]
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	260 file = $data_narrow_peak
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	261 #if $track.track_file_style_conditional.title:
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	262 title = $track.track_file_style_conditional.title
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	263 #elif $track.track_file_style_conditional.overlay_select == 'no':
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	264 title = $data_narrow_peak.name
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	265 #end if
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	266 color = $track.track_file_style_conditional.color
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	267 type = $track.track_file_style_conditional.display.display_selector
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	268 use_summit = $track.track_file_style_conditional.display.use_summit
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	269 #if $track.track_file_style_conditional.display.display_selector == "peak":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	270 show_data_range = $track.track_file_style_conditional.display.show_data
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	271 #if $track.track_file_style_conditional.display.width_adjust:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	272 width_adjust = $track.track_file_style_conditional.display.width_adjust
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	273 #end if
6 5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	274 #if $track.track_file_style_conditional.display.min_value != "":
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	275 min_value = $track.track_file_style_conditional.display.min_value
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	276 #end if
6 5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	277 #if $track.track_file_style_conditional.display.max_value != "":
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	278 max_value = $track.track_file_style_conditional.display.max_value
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	279 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	280 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	281 #if $track.track_file_style_conditional.height_narrow_peak:
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	282 height = $track.track_file_style_conditional.height_narrow_peak
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	283 #end if
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	284 line_width = $track.track_file_style_conditional.line_width
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	285 show_labels = $track.track_file_style_conditional.show_labels
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	286 file_type = narrow_peak
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	287 #if $track.track_file_style_conditional.fontsize:
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	288 fontsize = $track.track_file_style_conditional.fontsize
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	289 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	290 #if $track.track_file_style_conditional.invert_orientation:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	291 orientation = inverted
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	292 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	293 overlay_previous = $track.track_file_style_conditional.overlay_select
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	294 ## If spacer is asked a new section is created:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	295 #if $track.track_file_style_conditional.spacer_height != "":
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	296 [spacer]
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	297 height = $track.track_file_style_conditional.spacer_height
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	298 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	299 #end for
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	300 #end if
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	301
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	302 ## Bedgraph track
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	303 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	304 #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	305 [bedgraph_$counter]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	306 file = $data_bedgraph
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	307 #if $track.track_file_style_conditional.title:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	308 title = $track.track_file_style_conditional.title
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	309 #elif $track.track_file_style_conditional.overlay_select == "no":
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	310 title = $data_bedgraph.name
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	311 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	312 #if $track.track_file_style_conditional.color:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	313 color = $track.track_file_style_conditional.color
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	314 #end if
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	315 alpha = $track.track_file_style_conditional.alpha
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	316 #if $track.track_file_style_conditional.color_negative.color_negative_select == "true":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	317 negative_color = $track.track_file_style_conditional.color_negative.color
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	318 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	319 #if $track.track_file_style_conditional.height_bedgraph:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	320 height = $track.track_file_style_conditional.height_bedgraph
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	321 #end if
6 5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	322 #if $track.track_file_style_conditional.min_value != "":
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	323 min_value = $track.track_file_style_conditional.min_value
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	324 #end if
6 5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	325 #if $track.track_file_style_conditional.max_value != "":
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	326 max_value = $track.track_file_style_conditional.max_value
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	327 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	328 show_data_range = $track.track_file_style_conditional.show_data
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	329 grid = $track.track_file_style_conditional.grid
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	330 nans_to_zeros = $track.track_file_style_conditional.nans_to_zeros
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	331 use_middle = $track.track_file_style_conditional.use_middle
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	332 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	333 #if $columns > 4:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	334 file_type = bedgraph_matrix
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	335 type = lines
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	336 #else:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	337 file_type = bedgraph
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	338 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option':
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	339 type = fill
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	340 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option':
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	341 type = line:$track.track_file_style_conditional.type_conditional.width_line
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	342 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	343 type = points:$track.track_file_style_conditional.type_conditional.width_point
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	344 #end if
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	345 #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'no':
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	346 transform = $track.track_file_style_conditional.logScale_conditional.transform_selector
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	347 y_axis_values = $track.track_file_style_conditional.logScale_conditional.y_axis_values
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	348 #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'log1p':
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	349 log_pseudocount = $track.track_file_style_conditional.logScale_conditional.log_pseudocount
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	350 #end if
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	351 #end if
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	352 #end if
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	353 #if $track.track_file_style_conditional.reading_bdg_as_bw.summary_method != 'no':
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	354 summary_method = $track.track_file_style_conditional.reading_bdg_as_bw.summary_method
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	355 #if $track.track_file_style_conditional.reading_bdg_as_bw.number_of_bins:
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	356 number_of_bins = $track.track_file_style_conditional.reading_bdg_as_bw.number_of_bins
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	357 #end if
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	358 #end if
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	359 #if $track.track_file_style_conditional.op.operation != 'file':
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	360 operation = $track.track_file_style_conditional.op.operation
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	361 #if 'second_file' in str($track.track_file_style_conditional.op.operation):
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	362 second_file = $track.track_file_style_conditional.op.second_file
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	363 #end if
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	364 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	365 #if $track.track_file_style_conditional.invert_orientation:
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	366 orientation = inverted
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	367 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	368 overlay_previous = $track.track_file_style_conditional.overlay_select
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	369 ## If spacer is asked a new section is created:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	370 #if $track.track_file_style_conditional.spacer_height != "":
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	371 [spacer]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	372 height = $track.track_file_style_conditional.spacer_height
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	373 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	374 #end for
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	375 #end if
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	376
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	377 ## Bigwig tracks
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	378 #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	379 #for $data_bigwig in $track.track_file_style_conditional.track_input_bigwig:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	380 [bigwig_$counter]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	381 file = $data_bigwig
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	382 #if $track.track_file_style_conditional.title:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	383 title = $track.track_file_style_conditional.title
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	384 #elif $track.track_file_style_conditional.overlay_select == "no":
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	385 title = $data_bigwig.name
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	386 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	387 #if $track.track_file_style_conditional.color:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	388 color = $track.track_file_style_conditional.color
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	389 #end if
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	390 alpha = $track.track_file_style_conditional.alpha
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	391 #if $track.track_file_style_conditional.color_negative.color_negative_select == "true":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	392 negative_color = $track.track_file_style_conditional.color_negative.color
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	393 #end if
6 5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	394 #if $track.track_file_style_conditional.min_value != "":
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	395 min_value = $track.track_file_style_conditional.min_value
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	396 #end if
6 5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	397 #if $track.track_file_style_conditional.max_value != "":
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	398 max_value = $track.track_file_style_conditional.max_value
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	399 #end if
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	400 height = $track.track_file_style_conditional.height_bigwig
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	401 summary_method = $track.track_file_style_conditional.reading_bw_conditional.summary_method
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	402 nans_to_zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	403 #if $track.track_file_style_conditional.reading_bw_conditional.number_of_bins:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	404 number_of_bins = $track.track_file_style_conditional.reading_bw_conditional.number_of_bins
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	405 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	406 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option':
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	407 type = fill
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	408 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option':
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	409 type = line:$track.track_file_style_conditional.type_conditional.width_line
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	410 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	411 type = points:$track.track_file_style_conditional.type_conditional.width_point
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	412 #end if
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	413 #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'no':
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	414 transform = $track.track_file_style_conditional.logScale_conditional.transform_selector
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	415 y_axis_values = $track.track_file_style_conditional.logScale_conditional.y_axis_values
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	416 #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'log1p':
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	417 log_pseudocount = $track.track_file_style_conditional.logScale_conditional.log_pseudocount
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	418 #end if
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	419 #end if
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	420 #if $track.track_file_style_conditional.op.operation != 'file':
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	421 operation = $track.track_file_style_conditional.op.operation
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	422 #if 'second_file' in $track.track_file_style_conditional.op.operation:
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	423 second_file = $track.track_file_style_conditional.op.second_file
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	424 #end if
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	425 #end if
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	426 show_data_range = $track.track_file_style_conditional.show_data
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	427 grid = $track.track_file_style_conditional.grid
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	428 file_type = bigwig
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	429 #if $track.track_file_style_conditional.invert_orientation:
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	430 orientation = inverted
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	431 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	432 overlay_previous = $track.track_file_style_conditional.overlay_select
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	433 ## If spacer is asked a new section is created:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	434 #if $track.track_file_style_conditional.spacer_height != "":
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	435 [spacer]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	436 height = $track.track_file_style_conditional.spacer_height
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	437 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	438 #end for
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	439 #end if
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	440
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	441 ## bedgraph_matrix
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	442 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	443 #for $data_bedgraph_matrix in $track.track_file_style_conditional.track_input_bedgraph_matrix:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	444 [bedgraph_matrix_$counter]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	445 file = $data_bedgraph_matrix
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	446 #if $track.track_file_style_conditional.title:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	447 title = $track.track_file_style_conditional.title
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	448 #else:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	449 title = $data_bedgraph_matrix.name
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	450 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	451 #if $track.track_file_style_conditional.height_bedgraph:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	452 height = $track.track_file_style_conditional.height_bedgraph
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	453 #end if
6 5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	454 #if $track.track_file_style_conditional.min_value != "":
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	455 min_value = $track.track_file_style_conditional.min_value
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	456 #end if
6 5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	457 #if $track.track_file_style_conditional.max_value != "":
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	458 max_value = $track.track_file_style_conditional.max_value
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	459 #end if
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	460 type = $track.track_file_style_conditional.type.type_selector
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	461 file_type = bedgraph_matrix
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	462 #if $track.track_file_style_conditional.type.type_selector == 'lines':
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	463 show_data_range = $track.track_file_style_conditional.type.show_data
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	464 plot_horizontal_lines = $track.track_file_style_conditional.type.plot_horizontal_lines
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	465 pos_score_in_bin = $track.track_file_style_conditional.type.pos_score_in_bin
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	466 #else
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	467 colormap = $track.track_file_style_conditional.type.colormap
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	468 #end if
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	469 #if $track.track_file_style_conditional.invert_orientation:
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	470 orientation = inverted
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	471 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	472 ## If spacer is asked a new section is created:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	473 #if $track.track_file_style_conditional.spacer_height != "":
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	474 [spacer]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	475 height = $track.track_file_style_conditional.spacer_height
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	476 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	477 #end for
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	478 #end if
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	479
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	480 ## Vlines:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	481 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	482 [vlines_$counter]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	483 file = $track.track_file_style_conditional.track_input_bed_single
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	484 line_width = $track.track_file_style_conditional.line_width
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	485 type = vlines
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	486 #end if
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	487
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	488 ## Hlines:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	489 #if $track.track_file_style_conditional.track_file_style_selector == "hlines_track_option":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	490 [hlines_$counter]
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	491 #if $track.track_file_style_conditional.title:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	492 title = $track.track_file_style_conditional.title
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	493 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	494 #if $track.track_file_style_conditional.height:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	495 height = $track.track_file_style_conditional.height
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	496 #end if
6 5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	497 #if $track.track_file_style_conditional.min_value != "":
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	498 min_value = $track.track_file_style_conditional.min_value
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	499 #end if
6 5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	500 #if $track.track_file_style_conditional.max_value != "":
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	501 max_value = $track.track_file_style_conditional.max_value
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	502 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	503 y_values = $track.track_file_style_conditional.y_values
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	504 show_data_range = $track.track_file_style_conditional.show_data
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	505 color = $track.track_file_style_conditional.color
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	506 alpha = $track.track_file_style_conditional.alpha
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	507 line_width = $track.track_file_style_conditional.line_width
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	508 line_style = $track.track_file_style_conditional.line_style
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	509 #if $track.track_file_style_conditional.invert_orientation:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	510 orientation = inverted
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	511 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	512 overlay_previous = $track.track_file_style_conditional.overlay_select
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	513 file_type = hlines
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	514 ## If spacer is asked a new section is created:
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	515 #if $track.track_file_style_conditional.spacer_height != "":
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	516 [spacer]
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	517 height = $track.track_file_style_conditional.spacer_height
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	518 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	519 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	520
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	521 ## Spacer
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	522 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	523 [spacer]
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	524 #if $track.track_file_style_conditional.title:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	525 title = $track.track_file_style_conditional.title
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	526 #end if
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	527 #if $track.track_file_style_conditional.spacer_height != "":
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	528 height = $track.track_file_style_conditional.spacer_height
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	529 #end if
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	530 #end if
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	531
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	532 ## Xaxis:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	533 #if $track.track_file_style_conditional.track_file_style_selector == "xaxis_option":
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	534 [x-axis]
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	535 #if $track.track_file_style_conditional.title:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	536 title = $track.track_file_style_conditional.title
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	537 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	538 #if $track.track_file_style_conditional.fontsize != "":
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	539 fontsize = $track.track_file_style_conditional.fontsize
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	540 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	541 where = $track.track_file_style_conditional.xaxis_where
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	542 ## If spacer is asked a new section is created:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	543 #if $track.track_file_style_conditional.spacer_height != "":
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	544 [spacer]
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	545 height = $track.track_file_style_conditional.spacer_height
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	546 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	547 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	548
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	549 ## Scale bar:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	550 #if $track.track_file_style_conditional.track_file_style_selector == "scale_bar_option":
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	551 [scale_bar]
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	552 #if $track.track_file_style_conditional.title:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	553 title = $track.track_file_style_conditional.title
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	554 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	555 #if $track.track_file_style_conditional.color != "":
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	556 color = $track.track_file_style_conditional.color
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	557 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	558 alpha = $track.track_file_style_conditional.alpha
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	559 line_width = $track.track_file_style_conditional.line_width
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	560 #if $track.track_file_style_conditional.x_center != "":
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	561 x_center = $track.track_file_style_conditional.x_center
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	562 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	563 #if $track.track_file_style_conditional.size != "":
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	564 size = $track.track_file_style_conditional.size
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	565 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	566 where = $track.track_file_style_conditional.sb_where
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	567 #if $track.track_file_style_conditional.fontsize != "":
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	568 fontsize = $track.track_file_style_conditional.fontsize
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	569 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	570 file_type = scalebar
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	571 ## If spacer is asked a new section is created:
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	572 #if $track.track_file_style_conditional.spacer_height != "":
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	573 [spacer]
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	574 height = $track.track_file_style_conditional.spacer_height
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	575 #end if
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	576 #end if
1 0ea86f6bf2a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit f834c2a294c002123ef0613dc703aca00201b5bf iuc parents: 0 diff changeset	577 #end for
0ea86f6bf2a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit f834c2a294c002123ef0613dc703aca00201b5bf iuc parents: 0 diff changeset	578 </configfile>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	579 </configfiles>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	580 <inputs>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	581 <!--Arguments for pgt-->
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	582 <param argument="--region" type="text" label="Region of the genome to limit the operation" optional="false"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	583 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	584 <section name="global_args" title="Configure figure parameters" expanded="False">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	585 <param argument="--title" type="text" label="Plot title" help="If set, you may need to start by a spacer track"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	586 <param argument="--fontsize" type="integer" label="Font size for the labels of the plot" value="12"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	587 <param argument="--dpi" type="integer" label="Resolution (dpi)" value="72"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	588 help="Resolution for the image in case the ouput is a raster graphics image (e.g png, jpg)"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	589 <param argument="--trackLabelFraction" type="float" label="Proportion of space dedicated to track labels" value="0.05"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	590 min="0" max="1"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	591 <param argument="--trackLabelHAlign" type="select" label="Horizontal alignment of track labels">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	592 <option value="left" selected="True">left</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	593 <option value="right">right</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	594 <option value="center">center</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	595 </param>
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	596 <param argument="--decreasingXAxis" type="boolean" truevalue="--decreasingXAxis" falsevalue="" checked="false"
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	597 label="Use a decreasing x axis" help="By default, the x-axis is increasing. Use this option if you want to see all tracks with a decreasing x-axis."/>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	598 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	599 <!--Info to build the config file-->
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	600 <repeat name="tracks" min="1" title="Include tracks in your plot"
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	601 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph.
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	602 The order you add them represent the order they will be plotted from top to bottom.">
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	603 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	604 <param name="track_file_style_selector" type="select" label="Choose style of the track">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	605 <option value="hic_matrix_option">TAD visualization</option>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	606 <option value="chrom_states_option">Chromatine states</option>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	607 <option value="bedgraph_matrix_track_option">TAD score</option>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	608 <option value="gene_track_option">Gene track / Bed track</option>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	609 <option value="link_track_option">Link track</option>
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	610 <option value="narrow_peak_track_option">NarrowPeak track</option>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	611 <option value="bigwig_track_option">Bigwig track</option>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	612 <option value="bedgraph_track_option">Bedgraph track </option>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	613 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	614 <option value="vlines_track_option">Vlines track</option>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	615 <option value="hlines_track_option">Hlines track</option>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	616 <option value="spacer_option">Spacer</option>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	617 <option value="xaxis_option">X-axis</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	618 <option value="scale_bar_option">Scale bar track</option>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	619 </param>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	620 <when value="hic_matrix_option">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	621 <expand macro="plot_title" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	622 <expand macro="matrix_h5_cooler_multiple_macro" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	623
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	624 <param name="colormap" type="select" label="Color map to use for the heatmap" help="Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	625 <option value="RdYlBu_r">RdYlBu reversed</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	626 <expand macro="colormap_macro"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	627 </param>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	628 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	629 <expand macro="minmax_macro" />
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	630 <param name="transform" type="select" label="Plot the transformed value">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	631 <option value="log1p" selected="True" >log1p</option>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	632 <option value="log">log</option>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	633 <option value="-log">-log</option>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	634 <option value="no">no transformation</option>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	635
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	636 </param>
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	637 <param name="height_matrix" type="float" value="" optional="True" label="height"/>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	638 <param name="show_masked_bins" type="boolean" truevalue="true" falsevalue="false" checked="false"
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	639 label="Show masked bins" />
6 5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	640 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple="True"/>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	641 <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" />
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	642 <param name="rasterize" type="boolean" truevalue="true" falsevalue="false" checked="true"
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	643 label="Rasterize the heatmap" />
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	644 <expand macro="inverted_macro" />
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	645 <expand macro="spacer_macro" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	646
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	647 </when>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	648 <when value="chrom_states_option">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	649 <expand macro="plot_title" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	650 <expand macro="track_input_bed_macro" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	651 <conditional name="color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	652 <param name="color_bed_select" type="select" label="Define color:">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	653 <option value="manually" selected="True">manually</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	654 <option value="bed_rgb">From the 9th field</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	655 <option value="colormap">From the 5th field (score)</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	656 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	657 <when value="manually">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	658 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	659 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	660 <when value="bed_rgb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	661 <when value="colormap">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	662 <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	663 <expand macro="colormap_macro" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	664 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	665 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	666 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	667 <expand macro="border_color_bed_macro" />
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	668 <param name="line_width" type="float" value="0.5" label="width of lines" />
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	669 <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	670 <param name="labels" type="boolean" truevalue="true" falsevalue="false" checked="true"
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	671 label="Plot labels" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	672 <expand macro="spacer_macro" />
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	673
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	674 </when>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	675 <when value="gene_track_option">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	676 <expand macro="plot_title" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	677
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	678 <expand macro="track_input_bed_gtf_macro" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	679 <conditional name="color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	680 <param name="color_bed_select" type="select" label="Define color:">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	681 <option value="manually" selected="True">manually</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	682 <option value="bed_rgb">From the 9th field</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	683 <option value="colormap">From the 5th field (score)</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	684 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	685 <when value="manually">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	686 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	687 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	688 <when value="bed_rgb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	689 <when value="colormap">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	690 <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	691 <expand macro="colormap_macro" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	692 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	693 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	694 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	695 <expand macro="border_color_bed_macro" />
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	696 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	697 <conditional name="labels">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	698 <param name="plot_labels" type="select" label="Plot labels">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	699 <option value="true" selected="True">yes</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	700 <option value="false">no</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	701 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	702 <when value="true">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	703 <param name="all_labels_inside" type="boolean" truevalue="true" falsevalue="false" checked="false"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	704 label="Put all labels inside the plotted region"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	705 help="Put labels on the left of the region if the region ends after the plotted region."/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	706 <param name="labels_in_margin" type="boolean" truevalue="true" falsevalue="false" checked="false"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	707 label="Allow to put labels in the right margin"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	708 help="Put labels in the margin if the region ends after the plotted region."/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	709 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	710 <when value="false"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	711 </conditional>
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	712 <param name="display" type="select" label="display to use">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	713 <option value="stacked" selected="True">stacked (no overlap even with the label)</option>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	714 <option value="interleaved">interleaved (everything on 2 lines)</option>
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	715 <option value="collapsed">collapsed (everything on 1 line)</option>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	716 <option value="triangles">triangles (plot triangles between start and end)</option>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	717 </param>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	718 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	719 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	720 <param name="bed_style_select" type="select" label="Bed style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	721 <option value="flybase" selected="True">flybase (blocks with arrow at extremities)</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	722 <option value="UCSC">UCSC (blocks with arrows in introns)</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	723 <option value="tssarrow">tssarrow (blocks with arrow above at beginning)</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	724 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	725 <when value="flybase">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	726 <param name="arrowhead_included" type="boolean" truevalue="true" falsevalue="false" checked="false"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	727 label="Include the arrowhead in the bed interval:"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	728 help="When set to False, the arrow indicating the orientation of the interval is plotted outside of the interval."/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	729 <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	730 <expand macro="utr_macro" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	731 <expand macro="bed_advanced_macro" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	732 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	733 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	734 <when value="UCSC">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	735 <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	736 <param name="arrow_interval" type="integer" value="2" min="0" label="interval between 2 arrows on introns in UCSC style"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	737 <expand macro="bed_advanced_macro" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	738 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	739 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	740 <when value="tssarrow">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	741 <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	742 <param name="arrow_length" type="integer" optional="true" label="arrow length" help="the length of the arrow in bp (default is 4% of the plotted region)"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	743 <expand macro="utr_macro" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	744 <expand macro="bed_advanced_macro" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	745 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	746 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	747 </conditional>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	748 <expand macro="overlay_macro" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	749 <expand macro="inverted_macro" />
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	750 <expand macro="spacer_macro" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	751
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	752 </when>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	753 <when value="link_track_option">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	754 <expand macro="plot_title" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	755 <expand macro="track_input_link_macro" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	756 <conditional name="color_link">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	757 <param name="color_link_select" type="select" label="Define color:">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	758 <option value="manually" selected="True">manually</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	759 <option value="colormap">From the 7th field (score)</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	760 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	761 <when value="manually">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	762 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	763 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	764 <when value="colormap">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	765 <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	766 <expand macro="colormap_macro" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	767 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	768 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	769 </conditional>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	770 <expand macro="lines_macro" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	771 <param name="links_type" type="select" label="Representation of the link:">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	772 <option value="arcs" selected="True">arcs (a line between the centers of the 2 regions)</option>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	773 <option value="triangles">triangles</option>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	774 <option value="loops">loops (a rectangle highlighting the intersection)</option>
6 5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	775 </param>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	776 <param name="compact_arcs_level" type="select" label="Height of arcs and triangles:">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	777 <option value="0" selected="True">default (proportional to distance)</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	778 <option value="1">compacted (the height is proportional to the square root of the distance)</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	779 <option value="2">highly compacted (the height is the same for all distances)</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	780 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	781 <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/>
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	782 <param name="use_middle" type="select" label="Coordinates to use" help="Not useful with loops">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	783 <option value="false" selected="True">Extremities (start of first and end of second)</option>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	784 <option value="true">Center (mean of start and end for each)</option>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	785 </param>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	786 <param name="height" type="float" value="1.5" optional="True" label="height"/>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	787 <expand macro="minmax_macro" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	788 <expand macro="overlay_macro" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	789 <expand macro="inverted_macro" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	790 <expand macro="spacer_macro" />
6 5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	791 </when>
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	792 <when value="narrow_peak_track_option">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	793 <expand macro="plot_title" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	794 <expand macro="track_input_narrow_peak_macro" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	795 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	796 <param name="height_narrow_peak" type="float" value="1.5" optional="True" label="height"/>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	797 <conditional name="display">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	798 <param name="display_selector" type="select" label="display to use">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	799 <option value="peak" selected="True">peak: Draw a peak shape from start, end, summit, height</option>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	800 <option value="box">box: Draw a box</option>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	801 </param>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	802 <when value="peak">
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	803 <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true"
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	804 optional="True" label="Use summit information to make the curve." />
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	805 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false"
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	806 label="Show visualization of data range" />
6 5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	807 <param name="width_adjust" type="float" value="1.5" optional="True"
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	808 label="Factor to change the width of the curve."/>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	809 <expand macro="minmax_macro" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	810 </when>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	811 <when value="box">
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	812 <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true"
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	813 optional="True" label="Plot a vertical bar at the summit position." />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	814 </when>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	815 </conditional>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	816 <param name="line_width" type="float" value="1" label="width of lines" />
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	817 <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="true"
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	818 label="Plot labels (name, p-val, q-val)" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	819 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	820 <expand macro="overlay_macro" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	821 <expand macro="inverted_macro" />
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	822 <expand macro="spacer_macro" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	823
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	824 </when>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	825 <when value="bedgraph_track_option">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	826 <expand macro="plot_title" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	827 <expand macro="track_input_bedgraph_macro" />
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	828 <expand macro="color_coverage_macro" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	829 <expand macro="minmax_macro" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	830 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	831 <expand macro="type_coverage_macro" />
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	832 <section name="reading_bdg_as_bw" title="Configure bigwig parameters" expanded="False">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	833 <param name="summary_method" type="select" label="Summary method">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	834 <option value="no" selected="True">no=no summary method (keep all values)</option>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	835 <option value="mean">mean=mean value</option>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	836 <option value="min">min=minimum value</option>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	837 <option value="max">max=maximum value</option>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	838 <option value="coverage">coverage=number of covered bases</option>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	839 <option value="std">std=standard deviation</option>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	840 </param>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	841 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	842 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	843 <expand macro="logScale_coverage_macro" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	844 <section name ="op" title="Compute an operation on the file" expanded="False">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	845 <param name="operation" type="text" label="operation to compute on the file(s)" value="file"
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	846 help="operation will be evaluated, it should contains file or file and second_file, for example `0.89 * file` `- file` `file - second_file` `log2((1 + file) / (1 + second_file))` or `max(file, second_file)`"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	847 <param name="second_file" type="data" format="bedgraph" label="second_file (bedgraph format)" multiple="False" optional="True"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	848 </section>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	849 <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false"
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	850 label="NAN's to zeros" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	851 <param name="use_middle" type="boolean" truevalue="true" falsevalue="false" checked="false"
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	852 label="Use middle: Instead of using start and end, use the middle of intervals (useful for 4C-seq tracks)." />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	853 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" />
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	854 <param name="grid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Display a grid on the y-axis" />
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	855 <expand macro="inverted_macro" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	856 <expand macro="overlay_macro" />
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	857 <expand macro="spacer_macro" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	858 </when>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	859 <when value="bigwig_track_option">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	860 <expand macro="plot_title" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	861
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	862 <expand macro="track_input_bigwig_macro" />
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	863 <expand macro="color_coverage_macro" />
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	864
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	865 <expand macro="minmax_macro" />
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	866
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	867 <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	868 <section name="reading_bw_conditional" title="Configure bigwig parameters" expanded="False">
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	869 <param name="summary_method" type="select" label="Summary method">
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	870 <option value="mean" selected="True">mean=mean value</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	871 <option value="min">min=minimum value</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	872 <option value="max">max=maximum value</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	873 <option value="coverage">coverage=number of covered bases</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	874 <option value="std">std=standard deviation</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	875 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	876 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	877 <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	878 label="NAN's to zeros" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	879 </section>
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	880 <expand macro="type_coverage_macro" />
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	881 <expand macro="logScale_coverage_macro" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	882 <section name ="op" title="Compute an operation on the file" expanded="False">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	883 <param name="operation" type="text" label="operation to compute on the file(s)" value="file"
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	884 help="operation will be evaluated, it should contains file or file and second_file, for example `0.89 * file` `- file` `file - second_file` `log2((1 + file) / (1 + second_file))` or `max(file, second_file)`"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	885 <param name="second_file" type="data" format="bigwig" label="second_file (bedgraph format)" multiple="False" optional="True"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	886 </section>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	887 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/>
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	888 <param name="grid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Display a grid on the y-axis" />
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	889 <expand macro="inverted_macro" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	890 <expand macro="overlay_macro" />
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	891 <expand macro="spacer_macro" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	892
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	893 </when>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	894
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	895 <when value="bedgraph_matrix_track_option">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	896 <expand macro="plot_title" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	897
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	898 <expand macro="track_input_bedgraph_matrix_macro" />
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	899 <expand macro="minmax_macro" />
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	900
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	901 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	902
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	903 <conditional name="type">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	904 <param name="type_selector" type="select" label="type of plotting">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	905 <option value="lines" selected="True">lines: each column in the bedgraph will be a line and a mean line will be added</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	906 <option value="matrix">matrix: each column in the bedgraph will be a raw in the matrix</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	907 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	908 <when value="lines">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	909 <param name="plot_horizontal_lines" type="boolean" truevalue="true" falsevalue="false" checked="false"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	910 label="Plot an horizontal line at 0 when type is lines" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	911 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	912 label="Show visualization of data range" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	913 <param name="pos_score_in_bin" type="select" label="Position of the score with respect to bin start and end">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	914 <option value="center" selected="True">Center</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	915 <option value="block">Block (draw a horizontal line between start and end)</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	916 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	917 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	918 <when value="matrix">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	919 <param name="colormap" type="select" label="colormap">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	920 <option value="viridis">Viridis</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	921 <expand macro="colormap_macro" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	922 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	923 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	924 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	925
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	926
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	927 <expand macro="inverted_macro" />
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	928 <expand macro="spacer_macro" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	929
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	930 </when>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	931 <when value="vlines_track_option">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	932 <expand macro="track_input_bed_single_macro" />
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	933 <param name="line_width" type="float" value="0.5" label="width of lines"/>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	934 </when>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	935 <when value="hlines_track_option">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	936 <expand macro="plot_title" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	937 <param name="y_values" type="text" value="10, 200" label="Values where horizontal lines should be plotted separated by comma"/>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	938 <param name="color" type="color" value="#000000" label="Color of line(s)" optional="True" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	939 <expand macro="lines_macro" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	940 <param name="height" type="float" value="1.5" optional="True" label="height"/>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	941 <expand macro="minmax_macro" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	942 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	943 <expand macro="inverted_macro" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	944 <expand macro="overlay_macro" />
6 5cec5fb749f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf" iuc parents: 5 diff changeset	945 <expand macro="spacer_macro" />
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	946 </when>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	947 <when value="spacer_option">
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	948 <expand macro="plot_title" />
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	949 <param name="spacer_height" type="float" value="" optional="True"
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	950 label="Height of the spacer."/>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	951 </when>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	952 <when value="xaxis_option">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	953 <expand macro="plot_title" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	954 <param name="fontsize" type="float" optional="True"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	955 label="Fontsize of the x-axis."/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	956 <param name="xaxis_where" type="select" label="chromosome name and coordinates position relative to the axis">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	957 <option value="bottom" selected="True">below</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	958 <option value="top">above</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	959 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	960 <expand macro="spacer_macro" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	961 </when>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	962 <when value="scale_bar_option">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	963 <expand macro="plot_title" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	964 <param name="color" type="color" label="Color of the scale bar" optional="True" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	965 <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	966 <param name="line_width" type="float" value="0.5" label="width of lines"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	967 <param name="x_center" type="integer" label="coordinate where the scale bar should be plotted (center)" optional="True"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	968 help="If not set it will be in the middle of the plotted area."/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	969 <param name="size" type="integer" label="size of the scale bar" optional="True"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	970 help="If not set it will be the higher number that begins with 1, 2 or 5 followed by 0s that is less than half the plotted area."/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	971 <param name="sb_where" type="select" label="where the size of the scale bar should appear relative to the bar">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	972 <option value="left" selected="True">left</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	973 <option value="right">right</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	974 <option value="bottom">below</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	975 <option value="top">above</option>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	976 </param>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	977 <param name="fontsize" type="float" optional="True"
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	978 label="Fontsize of the size of the scale bar."/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	979 <expand macro="spacer_macro" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	980 </when>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	981 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	982 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	983 <param name="image_file_format" type="select" label="Image output format">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	984 <option value="png">png</option>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	985 <option value="svg">svg</option>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	986 </param>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	987 </inputs>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	988 <outputs>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	989 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on [${on_string}]: Plot">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	990 <change_format>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	991 <when input="image_file_format" value="png" format="png" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	992 <when input="image_file_format" value="svg" format="svg" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	993 </change_format>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	994 </data>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	995 </outputs>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	996 <tests>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	997 <!--test 1-->
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	998 <test>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	999 <param name="region" value="chrX:3000000-3500000"/>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1000 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1001 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1002 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1003 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1004 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1005 </repeat>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1006 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1007 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1008 <param name="track_file_style_selector" value="hic_matrix_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1009 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1010 <param name="title" value="Kc DpnII (Li et al. 2015)" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1011 <!--<param name="colormap" value="RdYlBu_r" />-->
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1012 <param name="depth" value="200000" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1013 <param name="transform" value="log1p" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1014 <param name="boundaries_file" value="domains.bed" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1015 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1016 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1017 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1018 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1019 <param name="track_file_style_selector" value="spacer_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1020 <param name="spacer_height" value="0.05" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1021 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1022 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1023 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1024 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1025 <param name="track_file_style_selector" value="chrom_states_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1026 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1027 <param name="title" value="TAD state" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1028 <param name="height_chrom" value="0.5" />
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1029 <param name="labels" value="false" />
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1030 <conditional name="color_bed">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1031 <param name="color_bed_select" value="bed_rgb" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1032 </conditional>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1033 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1034 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1035 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1036 <conditional name="track_file_style_conditional">
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1037 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1038 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" />
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1039 <param name="title" value="TAD separation score (Ramirez et al.)" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1040 <conditional name="type">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1041 <param name="type_selector" value="matrix" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1042 <!--<param name="colormap" value="viridis" />-->
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1043 </conditional>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1044 <param name="height_bedgraph" value="10" />
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1045 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1046 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1047 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1048 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1049 <param name="track_file_style_selector" value="spacer_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1050 <param name="spacer_height" value="1" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1051 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1052 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1053 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1054 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1055 <param name="track_file_style_selector" value="bedgraph_track_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1056 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1057 <param name="title" value="bedgraph" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1058 <param name="height_bedgraph" value="4" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1059 <param name="color" value="blue" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1060 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1061 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1062 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1063 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1064 <param name="track_file_style_selector" value="bigwig_track_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1065 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1066 <param name="title" value="rep 1 test fill" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1067 <param name="height_bigwig" value="4" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1068 <param name="color" value="blue" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1069 <conditional name="type_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1070 <param name="type_selector" value="fill_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1071 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1072 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1073 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1074 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1075 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1076 <param name="track_file_style_selector" value="bigwig_track_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1077 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1078 <param name="title" value="rep 1 test line" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1079 <param name="height_bigwig" value="4" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1080 <param name="color" value="red" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1081 <conditional name="type_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1082 <param name="type_selector" value="line_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1083 <param name="width_line" value="1" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1084 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1085 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1086 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1087 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1088 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1089 <param name="track_file_style_selector" value="bigwig_track_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1090 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1091 <param name="title" value="rep 1 test lw=0.2" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1092 <param name="height_bigwig" value="4" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1093 <param name="color" value="red" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1094 <conditional name="type_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1095 <param name="type_selector" value="line_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1096 <param name="width_line" value="0.1" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1097
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1098 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1099 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1100 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1101 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1102 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1103 <param name="track_file_style_selector" value="bigwig_track_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1104 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1105 <param name="title" value="rep 1 test point:0.5" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1106 <param name="height_bigwig" value="4" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1107 <param name="color" value="black" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1108 <conditional name="type_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1109 <param name="type_selector" value="point_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1110 <param name="width_point" value="0.5" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1111
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1112 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1113 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1114 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1115 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1116 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1117 <param name="track_file_style_selector" value="spacer_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1118 <param name="spacer_height" value="0.5" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1119 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1120 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1121 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1122 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1123 <param name="track_file_style_selector" value="gene_track_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1124 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1125 <param name="title" value="genes" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1126 <param name="height_bed" value="5" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1127 <param name="fontsize" value="10" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1128 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1129 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1130 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1131 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1132 <param name="track_file_style_selector" value="spacer_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1133 <param name="spacer_height" value="1" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1134 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1135 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1136 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1137 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1138 <param name="track_file_style_selector" value="gene_track_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1139 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1140 <param name="title" value="max num rows 3" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1141 <param name="height_bed" value="3" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1142 <param name="fontsize" value="8" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1143 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1144 <section name="bed_advanced">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1145 <param name="gene_rows" value="3" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1146 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1147 </conditional>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1148 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1149 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1150 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1151 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1152 <param name="track_file_style_selector" value="spacer_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1153 <param name="spacer_height" value="1" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1154 </conditional>
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1155 </repeat>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1156 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1157 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1158 <param name="track_file_style_selector" value="gene_track_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1159 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1160 <param name="title" value="bed6 global max row" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1161 <param name="height_bed" value="20" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1162 <param name="fontsize" value="10" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1163 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1164 <section name="bed_advanced">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1165 <param name="global_max_row" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1166 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1167 </conditional>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1168 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1169 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1170 <repeat name="tracks">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1171 <conditional name="track_file_style_conditional">
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1172 <param name="track_file_style_selector" value="vlines_track_option" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1173 <param name="track_input_bed_single" value="domains.bed" ftype="bed" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1174 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1175 </repeat>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1176 <param name="image_file_format" value="png" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1177 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1178 </test>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1179 <!--test 2-->
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1180 <test>
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1181 <param name="region" value="chrX:3000000-3500000"/>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1182 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1183 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1184 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1185 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1186 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1187 </repeat>
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1188 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1189 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1190 <param name="track_file_style_selector" value="bigwig_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1191 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw,bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1192 <param name="title" value="rep 1 test line" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1193 <param name="height_bigwig" value="4" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1194 <param name="color" value="red" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1195 <conditional name="type_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1196 <param name="type_selector" value="line_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1197 <param name="width_line" value="1" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1198 </conditional>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1199 </conditional>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1200 </repeat>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1201 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1202 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1203 <param name="track_file_style_selector" value="bigwig_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1204 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1205 <param name="title" value="nans_to_zeros" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1206 <param name="height_bigwig" value="4" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1207 <param name="color" value="blue" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1208 <section name="reading_bw_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1209 <param name="nans_to_zeros" value="true" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1210 </section>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1211 <param name="show_data" value="true" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1212 <conditional name="type_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1213 <param name="type_selector" value="line_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1214 <param name="width_line" value="1" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1215 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1216 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1217 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1218 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1219 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1220 <param name="track_file_style_selector" value="hlines_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1221 <param name="title" value="" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1222 <param name="color" value="orange" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1223 <param name="y_values" value="50" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1224 <param name="line_width" value="2" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1225 <param name="line_style" value="dashed" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1226 <param name="overlay_select" value="share-y" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1227 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1228 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1229 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1230 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1231 <param name="track_file_style_selector" value="hlines_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1232 <param name="title" value="hlines" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1233 <param name="color" value="purple" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1234 <param name="y_values" value="0, 10, 20, 100" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1235 <param name="min_value" value="12" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1236 <param name="show_data" value="true" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1237 <param name="invert_orientation" value="true" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1238 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1239 </repeat>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1240 <param name="image_file_format" value="png" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1241 <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	1242 </test>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1243 <!--test 3-->
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1244 <test>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1245 <param name="region" value="chrX:3000000-3500000"/>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1246 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1247 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1248 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1249 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1250 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1251 </repeat>
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1252 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1253 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1254 <param name="track_file_style_selector" value="hic_matrix_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1255 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1256 <param name="title" value="Kc DpnII (Li et al. 2015) log1p" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1257 <param name="colormap" value="RdYlBu_r" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1258 <param name="depth" value="200000" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1259 <param name="transform" value="log1p" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1260 <param name="boundaries_file" value="domains.bed" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1261 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1262 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1263 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1264 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1265 <param name="track_file_style_selector" value="chrom_states_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1266 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1267 <param name="title" value="TAD state" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1268 <param name="height_chrom" value="0.5" />
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1269 <param name="labels" value="false" />
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1270 <conditional name="color_bed">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1271 <param name="color_bed_select" value="bed_rgb" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1272 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1273 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1274 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1275 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1276 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1277 <param name="track_file_style_selector" value="hic_matrix_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1278 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1279 <param name="title" value="Kc DpnII (Li et al. 2015) inverted no transform" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1280 <param name="colormap" value="Reds" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1281 <param name="depth" value="200000" />
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1282 <param name="transform" value="no" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1283 <param name="invert_orientation" value="true" />
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1284 <param name="min_value" value="5" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1285 <param name="max_value" value="70" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1286 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1287 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1288 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1289 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1290 <param name="track_file_style_selector" value="spacer_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1291 <param name="spacer_height" value="1" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1292 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1293 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1294 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1295 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1296 <param name="track_file_style_selector" value="bedgraph_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1297 <param name="track_input_bedgraph" value="test_with_neg_values.bg.gz" ftype="bedgraph" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1298 <param name="title" value="bedgraph with negative values" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1299 <param name="height_bedgraph" value="4" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1300 <param name="color" value="black" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1301 <conditional name="color_negative">
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1302 <param name="color_negative_select" value="true" />
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1303 <param name="color" value="red" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1304 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1305 <conditional name="type_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1306 <param name="type_selector" value="fill_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1307 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1308 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1309 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1310 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1311 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1312 <param name="track_file_style_selector" value="bedgraph_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1313 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1314 <param name="title" value="bedgraph" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1315 <param name="height_bedgraph" value="4" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1316 <param name="color" value="blue" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1317 <conditional name="type_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1318 <param name="type_selector" value="fill_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1319 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1320 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1321 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1322 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1323 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1324 <param name="track_file_style_selector" value="bigwig_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1325 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1326 <param name="title" value="rep 1 test fill" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1327 <param name="height_bigwig" value="4" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1328 <param name="color" value="blue" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1329 <conditional name="type_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1330 <param name="type_selector" value="fill_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1331 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1332 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1333 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1334 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1335 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1336 <param name="track_file_style_selector" value="bigwig_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1337 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1338 <param name="title" value="(red points/width=5/max value/100 bins) overlayed with (dark red line/min value/30000 bins) overlayed with (black line/min value)" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1339 <param name="height_bigwig" value="10" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1340 <param name="color" value="red" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1341 <conditional name="type_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1342 <param name="type_selector" value="point_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1343 <param name="width_point" value="5" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1344 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1345 <section name="reading_bw_conditional">
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1346 <param name="summary_method" value="max"/>
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1347 <param name="number_of_bins" value="100"/>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1348 </section>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1349 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1350 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1351 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1352 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1353 <param name="track_file_style_selector" value="bigwig_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1354 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1355 <param name="height_bigwig" value="10" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1356 <param name="color" value="#c00000" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1357 <conditional name="type_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1358 <param name="type_selector" value="line_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1359 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1360 <section name="reading_bw_conditional">
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1361 <param name="summary_method" value="min"/>
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1362 </section>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1363 <param name="overlay_select" value="share-y" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1364 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1365 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1366 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1367 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1368 <param name="track_file_style_selector" value="bigwig_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1369 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1370 <param name="height_bigwig" value="10" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1371 <param name="color" value="black" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1372 <conditional name="type_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1373 <param name="type_selector" value="line_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1374 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1375 <section name="reading_bw_conditional">
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1376 <param name="summary_method" value="min"/>
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1377 <param name="number_of_bins" value="30000"/>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1378 </section>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1379 <param name="overlay_select" value="share-y" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1380 <param name="spacer_height" value="1" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1381 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1382 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1383 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1384 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1385 <param name="track_file_style_selector" value="gene_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1386 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1387 <param name="title" value="genes in ucsc" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1388 <param name="height_bed" value="5" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1389 <param name="fontsize" value="10" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1390 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1391 <param name="bed_style_select" value="UCSC"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1392 </conditional>
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1393 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1394 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1395 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1396 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1397 <param name="track_file_style_selector" value="gene_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1398 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1399 <param name="title" value="bed6 global max row color from score" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1400 <param name="height_bed" value="20" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1401 <param name="fontsize" value="10" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1402 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1403 <section name="bed_advanced">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1404 <param name="global_max_row" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1405 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1406 </conditional>
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1407 <conditional name="color_bed">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1408 <param name="color_bed_select" value="colormap" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1409 <param name="color" value="RdYlBu_r" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1410 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1411 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1412 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1413 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1414 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1415 <param name="track_file_style_selector" value="gene_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1416 <param name="track_input_bed" value="domains.bed" ftype="bed" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1417 <param name="title" value="domains.bed using the 9th field for colors interleaved border=red" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1418 <param name="height_bed" value="2" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1419 <param name="fontsize" value="10" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1420 <conditional name="color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1421 <param name="color_bed_select" value="bed_rgb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1422 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1423 <conditional name="border_color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1424 <param name="border_color_bed_select" value="manually" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1425 <param name="color" value="red" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1426 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1427 <conditional name="labels">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1428 <param name="plot_labels" value="false" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1429 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1430 <param name="display" value="interleaved" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1431 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1432 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1433 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1434 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1435 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1436 <param name="track_input_bed" value="domains.bed" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1437 <param name="title" value="domains.bed using the 9th field for colors interleaved border=bed_rgb" />
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1438 <param name="height_bed" value="2" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1439 <param name="fontsize" value="10" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1440 <conditional name="color_bed">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1441 <param name="color_bed_select" value="bed_rgb" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1442 </conditional>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1443 <conditional name="border_color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1444 <param name="border_color_bed_select" value="bed_rgb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1445 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1446 <conditional name="labels">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1447 <param name="plot_labels" value="false" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1448 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1449 <param name="display" value="interleaved" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1450 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1451 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1452 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1453 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1454 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1455 <param name="track_input_bed" value="domains.bed" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1456 <param name="title" value="domains.bed using the 9th field for colors interleaved border=none" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1457 <param name="height_bed" value="2" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1458 <param name="fontsize" value="10" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1459 <conditional name="color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1460 <param name="color_bed_select" value="bed_rgb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1461 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1462 <conditional name="border_color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1463 <param name="border_color_bed_select" value="none" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1464 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1465 <conditional name="labels">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1466 <param name="plot_labels" value="false" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1467 </conditional>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1468 <param name="display" value="interleaved" />
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1469 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1470 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1471 <param name="image_file_format" value="png" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1472 <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="35000" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1473 </test>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1474 <!--test 4-->
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1475 <test>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1476 <param name="region" value="X:2700000-3100000"/>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1477 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1478 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1479 <param name="track_file_style_selector" value="bigwig_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1480 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1481 <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1482 <param name="height_bigwig" value="7" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1483 <param name="color" value="#00b0f0" />
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1484 <section name="reading_bw_conditional">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1485 <param name="number_of_bins" value="2000"/>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1486 </section>
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1487 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1488 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1489 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1490 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1491 <param name="track_file_style_selector" value="bigwig_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1492 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1493 <param name="title" value="" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1494 <param name="color" value="#ff0000" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1495 <param name="alpha" value="0.5" />
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	1496 <param name="summary_method" value="max" />
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1497 <section name="reading_bw_conditional">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1498 <param name="number_of_bins" value="300"/>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1499 </section>
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1500 <param name="overlay_select" value="share-y"/>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1501 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1502 </repeat>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1503 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1504 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1505 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1506 <param name="xaxis_where" value="bottom" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1507 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1508 </repeat>
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1509 <param name="image_file_format" value="png" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1510 <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="35000" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1511 </test>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1512 <!--test 5-->
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1513 <test>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1514 <param name="region" value="X:3000000-3300000"/>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1515 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1516 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1517 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1518 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1519 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1520 </repeat>
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1521 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1522 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1523 <param name="track_file_style_selector" value="gene_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1524 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1525 <param name="title" value="test" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1526 <param name="height_bed" value="10" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1527 <param name="color" value="#000000" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1528 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1529 <param name="bed_style_select" value="UCSC"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1530 </conditional>
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1531 <param name="spacer_height" value="1"/>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1532 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1533 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1534 <repeat name="tracks">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1535 <conditional name="track_file_style_conditional">
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1536 <param name="track_file_style_selector" value="gene_track_option" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1537 <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1538 <param name="title" value="test" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1539 <param name="height_bed" value="10" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1540 <param name="color" value="#000000" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1541 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1542 <param name="bed_style_select" value="UCSC"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1543 </conditional>
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1544 <param name="spacer_height" value="1"/>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1545 </conditional>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1546 </repeat>
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1547 <param name="image_file_format" value="png" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1548 <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" />
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	1549 </test>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1550 <!--test 6-->
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1551 <test>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1552 <param name="region" value="X:2760000-2802000"/>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1553 <repeat name="tracks">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1554 <conditional name="track_file_style_conditional">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1555 <param name="track_file_style_selector" value="narrow_peak_track_option" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1556 <param name="title" value="box" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1557 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1558 <param name="color" value="#9bbb59" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1559 <param name="height_narrow_peak" value="4" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1560 <conditional name="display">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1561 <param name="display_selector" value="box" />
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1562 <param name="use_summit" value="true" />
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1563 </conditional>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1564 <param name="show_labels" value="true" />
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1565 </conditional>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1566 </repeat>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1567 <repeat name="tracks">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1568 <conditional name="track_file_style_conditional">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1569 <param name="track_file_style_selector" value="narrow_peak_track_option" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1570 <param name="title" value="box line_width = 2" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1571 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1572 <param name="color" value="#9bbb59" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1573 <param name="height_narrow_peak" value="4" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1574 <param name="line_width" value="2" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1575 <conditional name="display">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1576 <param name="display_selector" value="box" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1577 <param name="use_summit" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1578 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1579 <param name="show_labels" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1580 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1581 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1582 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1583 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1584 <param name="track_file_style_selector" value="narrow_peak_track_option" />
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1585 <param name="title" value="peak width 3" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1586 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1587 <param name="color" value="#c0504d" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1588 <param name="height_narrow_peak" value="4" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1589 <conditional name="display">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1590 <param name="display_selector" value="peak" />
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1591 <param name="use_summit" value="true" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1592 <param name="show_data" value="true" />
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1593 <param name="width_adjust" value="3" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1594 <param name="max_value" value="50" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1595 </conditional>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1596 <param name="show_labels" value="false" />
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1597 <param name="spacer_height" value="0.5"/>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1598 </conditional>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1599 </repeat>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1600 <repeat name="tracks">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1601 <conditional name="track_file_style_conditional">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1602 <param name="track_file_style_selector" value="narrow_peak_track_option" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1603 <param name="title" value="peak no data range" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1604 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1605 <param name="color" value="#000000" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1606 <param name="height_narrow_peak" value="4" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1607 <conditional name="display">
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1608 <param name="display_selector" value="peak" />
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1609 <param name="use_summit" value="false" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1610 <param name="show_data" value="false" />
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1611 </conditional>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1612 <param name="show_labels" value="true" />
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1613 </conditional>
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1614 </repeat>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1615 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1616 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1617 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1618 <param name="xaxis_where" value="bottom" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1619 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1620 </repeat>
4 c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1621 <param name="image_file_format" value="png" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1622 <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="35000" />
c237ba772225 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3" iuc parents: 3 diff changeset	1623 </test>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1624 <!--test 7-->
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1625 <test>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1626 <param name="region" value="chrX:3300000-3500000"/>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1627 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1628 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1629 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1630 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1631 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1632 </repeat>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1633 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1634 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1635 <param name="track_file_style_selector" value="gene_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1636 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1637 <param name="title" value="genes" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1638 <param name="height_bed" value="10" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1639 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1640 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1641 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1642 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1643 <param name="track_file_style_selector" value="gene_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1644 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1645 <param name="title" value="gtf" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1646 <param name="height_bed" value="10" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1647 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1648 <section name="bed_advanced">
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1649 <param name="height_utr" value="0.75"/>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1650 <conditional name="color_utr">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1651 <param name="color_utr_select" value="manually"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1652 <param name="color" value="#ff0000"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1653 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1654 <section name ="gtf">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1655 <param name="prefered_name" value="gene_name"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1656 <param name="merge_transcripts" value="true"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1657 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1658 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1659 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1660 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1661 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1662 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1663 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1664 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1665 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1666 <param name="title" value="genes with scores" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1667 <param name="height_bed" value="10" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1668 <conditional name="color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1669 <param name="color_bed_select" value="colormap" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1670 <param name="color" value="cool_r" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1671 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1672 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1673 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1674 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1675 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1676 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1677 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1678 <param name="title" value="genes with utr as bed_rgb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1679 <param name="height_bed" value="10" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1680 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1681 <section name="bed_advanced">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1682 <conditional name="color_utr">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1683 <param name="color_utr_select" value="bed_rgb"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1684 </conditional>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1685 </section>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1686 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1687 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1688 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1689 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1690 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1691 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1692 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1693 <param name="title" value="genes with coding as bed_rgb - labels_in_margin" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1694 <param name="height_bed" value="10" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1695 <conditional name="color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1696 <param name="color_bed_select" value="bed_rgb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1697 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1698 <conditional name="labels">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1699 <param name="plot_labels" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1700 <param name="labels_in_margin" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1701 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1702 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1703 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1704 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1705 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1706 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1707 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1708 <param name="title" value="genes bed_rgb like - all_labels_inside" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1709 <param name="height_bed" value="10" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1710 <conditional name="color_bed">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1711 <param name="color_bed_select" value="bed_rgb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1712 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1713 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1714 <section name="bed_advanced">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1715 <conditional name="color_utr">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1716 <param name="color_utr_select" value="like"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1717 </conditional>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1718 </section>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1719 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1720 <conditional name="labels">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1721 <param name="plot_labels" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1722 <param name="all_labels_inside" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1723 </conditional>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1724 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1725 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1726 <param name="image_file_format" value="png" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1727 <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="sim_size" delta="35000" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1728 </test>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1729 <!--test 8-->
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1730 <test>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1731 <param name="region" value="chrX:3300000-3500000"/>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1732 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1733 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1734 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1735 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1736 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1737 </repeat>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1738 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1739 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1740 <param name="track_file_style_selector" value="gene_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1741 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1742 <param name="title" value="dm3_genes.bed" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1743 <param name="height_bed" value="10" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1744 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1745 <param name="bed_style_select" value="UCSC"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1746 <section name="bed_advanced">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1747 <param name="global_max_row" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1748 <param name="max_labels" value="15" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1749 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1750 </conditional>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1751 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1752 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1753 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1754 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1755 <param name="track_file_style_selector" value="gene_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1756 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1757 <param name="title" value="genes.bed.gz" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1758 <param name="height_bed" value="10" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1759 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1760 <param name="bed_style_select" value="UCSC"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1761 <section name="bed_advanced">
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1762 <param name="arrow_interval" value="10"/>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1763 <param name="line_width" value="2"/>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1764 </section>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1765 </conditional>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1766 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1767 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1768 <param name="image_file_format" value="png" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1769 <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="sim_size" delta="35000" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1770 </test>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1771 <!--test 9-->
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1772 <test>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1773 <param name="region" value="X:3133000-3138000"/>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1774 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1775 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1776 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1777 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1778 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1779 </repeat>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1780 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1781 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1782 <param name="track_file_style_selector" value="gene_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1783 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1784 <param name="title" value="test" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1785 <param name="height_bed" value="10" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1786 <param name="spacer_height" value="1"/>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1787 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1788 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1789 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1790 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1791 <param name="track_file_style_selector" value="gene_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1792 <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1793 <param name="title" value="test" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1794 <param name="height_bed" value="10" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1795 <conditional name="color_bed">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1796 <param name="color_bed_select" value="manually" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1797 <param name="color" value="red" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1798 </conditional>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1799 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1800 <param name="bed_style_select" value="UCSC"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1801 </conditional>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1802 <param name="spacer_height" value="1"/>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1803 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1804 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1805 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1806 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1807 <param name="track_file_style_selector" value="gene_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1808 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1809 <param name="title" value="test" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1810 <param name="height_bed" value="10" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1811 <conditional name="color_bed">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1812 <param name="color_bed_select" value="manually" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1813 <param name="color" value="red" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1814 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1815 <param name="spacer_height" value="1"/>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1816 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1817 <param name="arrowhead_included" value="true"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1818 </conditional>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1819 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1820 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1821 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1822 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1823 <param name="track_file_style_selector" value="vlines_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1824 <param name="track_input_bed_single" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1825 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1826 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1827 <param name="image_file_format" value="png" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1828 <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="35000" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1829 </test>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1830 <!--test 10-->
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1831 <test>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1832 <param name="region" value="X:3340000-3380000"/>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1833 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1834 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1835 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1836 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1837 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1838 </repeat>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1839 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1840 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1841 <param name="track_file_style_selector" value="gene_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1842 <param name="track_input_bed" value="domains.bed" ftype="bed" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1843 <param name="height_bed" value="6" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1844 <conditional name="color_bed">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1845 <param name="color_bed_select" value="manually" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1846 <param name="color" value="yellow" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1847 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1848 <param name="display" value="triangles" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1849 <param name="spacer_height" value="1"/>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1850 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1851 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1852 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1853 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1854 <param name="track_file_style_selector" value="bedgraph_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1855 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1856 <param name="title" value="bedgraph" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1857 <param name="height_bedgraph" value="4" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1858 <param name="color" value="blue" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1859 <conditional name="type_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1860 <param name="type_selector" value="line_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1861 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1862 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1863 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1864 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1865 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1866 <param name="track_file_style_selector" value="bedgraph_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1867 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1868 <param name="title" value="bedgraph" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1869 <param name="height_bedgraph" value="4" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1870 <param name="color" value="blue" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1871 <param name="use_middle" value="true" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1872 <conditional name="type_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1873 <param name="type_selector" value="line_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1874 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1875 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1876 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1877 <param name="image_file_format" value="png" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1878 <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="35000" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1879 </test>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1880 <!--test 11-->
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1881 <test>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1882 <param name="region" value="chrX:3250000-3400000"/>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1883 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1884 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1885 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1886 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1887 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1888 </repeat>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1889 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1890 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1891 <param name="track_file_style_selector" value="hic_matrix_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1892 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1893 <param name="title" value="Kc DpnII (Li et al. 2015)" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1894 <!--<param name="colormap" value="RdYlBu_r" />-->
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1895 <param name="depth" value="100000" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1896 <param name="transform" value="log1p" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1897 <param name="show_masked_bins" value="true" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1898 <param name="scale_factor" value="2.0" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1899 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1900 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1901 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1902 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1903 <param name="track_file_style_selector" value="spacer_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1904 <param name="spacer_height" value="0.05" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1905 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1906 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1907 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1908 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1909 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1910 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1911 <param name="title" value="TAD separation score (Ramirez et al.)" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1912 <param name="height_bedgraph" value="10" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1913 <conditional name="type">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1914 <param name="type_selector" value="lines" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1915 <param name="pos_score_in_bin" value="block" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1916 <param name="plot_horizontal_lines" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1917 <param name="show_data" value="true" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1918 </conditional>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1919 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1920 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1921 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1922 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1923 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1924 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1925 <param name="title" value="TAD separation score (Ramirez et al.)" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1926 <param name="height_bedgraph" value="10" />
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1927 <conditional name="type">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1928 <param name="type_selector" value="lines" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1929 <param name="pos_score_in_bin" value="center" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1930 <param name="plot_horizontal_lines" value="false" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1931 </conditional>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1932 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1933 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1934 <param name="image_file_format" value="png" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1935 <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="35000" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1936 </test>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1937 <!--test 12-->
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1938 <test>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1939 <param name="region" value="chrX:3000000-3300000"/>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1940 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1941 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1942 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1943 <param name="xaxis_where" value="top" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1944 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1945 </repeat>
5 eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1946 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1947 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1948 <param name="track_file_style_selector" value="hic_matrix_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1949 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1950 <param name="title" value="Kc DpnII (Li et al. 2015)" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1951 <param name="colormap" value="Purples" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1952 <param name="depth" value="190000" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1953 <param name="transform" value="no" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1954 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1955 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1956 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1957 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1958 <param name="track_file_style_selector" value="link_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1959 <param name="track_input_link" value="test.arcs" ftype="bed" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1960 <param name="title" value="" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1961 <param name="line_width" value="10" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1962 <param name="links_type" value="loops" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1963 <conditional name="color_link">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1964 <param name="color_link_select" value="manually" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1965 <param name="color" value="red" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1966 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1967 <param name="overlay_select" value="share-y" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1968 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1969 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1970 <repeat name="tracks">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1971 <conditional name="track_file_style_conditional">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1972 <param name="track_file_style_selector" value="link_track_option" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1973 <param name="track_input_link" value="test.arcs" ftype="bed" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1974 <param name="title" value="" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1975 <param name="height" value="5" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1976 <conditional name="color_link">
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1977 <param name="color_link_select" value="colormap" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1978 <param name="color" value="hot" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1979 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1980 <param name="max_value" value="5"/>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1981 <param name="invert_orientation" value="true" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1982 </conditional>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1983 </repeat>
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1984 <param name="image_file_format" value="png" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1985 <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="35000" />
eca03db4f612 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95" iuc parents: 4 diff changeset	1986 </test>
7 326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1987 <!--test 13-->
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1988 <test>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1989 <param name="region" value="chrX:3000000-3300000"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1990 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1991 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1992 <param name="track_file_style_selector" value="link_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1993 <param name="track_input_link" value="test.arcs" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1994 <param name="title" value="default" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1995 <conditional name="color_link">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1996 <param name="color_link_select" value="manually" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1997 <param name="color" value="#000000" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1998 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	1999 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2000 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2001 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2002 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2003 <param name="track_file_style_selector" value="link_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2004 <param name="track_input_link" value="test.arcs" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2005 <param name="title" value="ylim 20kb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2006 <conditional name="color_link">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2007 <param name="color_link_select" value="manually" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2008 <param name="color" value="#000000" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2009 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2010 <param name="ylim" value="20000" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2011 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2012 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2013 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2014 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2015 <param name="track_file_style_selector" value="link_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2016 <param name="track_input_link" value="test.arcs" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2017 <param name="title" value="compacted" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2018 <conditional name="color_link">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2019 <param name="color_link_select" value="manually" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2020 <param name="color" value="#000000" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2021 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2022 <param name="compact_arcs_level" value="1" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2023 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2024 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2025 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2026 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2027 <param name="track_file_style_selector" value="link_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2028 <param name="track_input_link" value="test.arcs" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2029 <param name="title" value="highly compacted" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2030 <conditional name="color_link">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2031 <param name="color_link_select" value="manually" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2032 <param name="color" value="#000000" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2033 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2034 <param name="compact_arcs_level" value="2" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2035 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2036 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2037 <param name="image_file_format" value="png" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2038 <output name="outFileName" file="test_link2.png" ftype="png" compare="sim_size" delta="35000" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2039 </test>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2040 <!--test 14-->
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2041 <test>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2042 <param name="region" value="chrX:3000000-3300000"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2043 <section name="global_args">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2044 <param name="title" value="Scale bar"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2045 <param name="trackLabelFraction" value="0.5"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2046 <param name="trackLabelHAlign" value="center"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2047 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2048 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2049 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2050 <param name="track_file_style_selector" value="spacer_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2051 <param name="spacer_height" value="1.0" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2052 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2053 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2054 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2055 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2056 <param name="track_file_style_selector" value="scale_bar_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2057 <param name="title" value="default" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2058 <param name="spacer_height" value="1"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2059 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2060 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2061 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2062 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2063 <param name="track_file_style_selector" value="scale_bar_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2064 <param name="title" value="scalebar where = right x_center = 3200000 size = 100002 fontsize = 8 line_width =2 color = red alpha = 0.5" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2065 <param name="color" value="red"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2066 <param name="alpha" value="0.5"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2067 <param name="line_width" value="2"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2068 <param name="x_center" value="3200000"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2069 <param name="size" value="100002"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2070 <param name="sb_where" value="right"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2071 <param name="fontsize" value="8"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2072 <param name="spacer_height" value="4"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2073 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2074 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2075 <param name="image_file_format" value="png" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2076 <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="sim_size" delta="35000" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2077 </test>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2078 <!--test 15-->
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2079 <test>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2080 <param name="region" value="chrX:3300000-3500000"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2081 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2082 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2083 <param name="track_file_style_selector" value="xaxis_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2084 <param name="xaxis_where" value="bottom" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2085 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2086 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2087 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2088 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2089 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2090 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2091 <param name="title" value="flybase" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2092 <param name="height_bed" value="10" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2093 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2094 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2095 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2096 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2097 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2098 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2099 <param name="title" value="UCSC" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2100 <param name="height_bed" value="10" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2101 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2102 <param name="bed_style_select" value="UCSC"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2103 <section name="bed_advanced">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2104 <param name="arrow_interval" value="10"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2105 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2106 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2107 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2108 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2109 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2110 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2111 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2112 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2113 <param name="title" value="tssarrow" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2114 <param name="height_bed" value="10" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2115 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2116 <param name="bed_style_select" value="tssarrow"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2117 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2118 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2119 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2120 <repeat name="tracks">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2121 <conditional name="track_file_style_conditional">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2122 <param name="track_file_style_selector" value="gene_track_option" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2123 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2124 <param name="title" value="tssarrow 5kb" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2125 <param name="height_bed" value="10" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2126 <conditional name="bed_style">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2127 <param name="bed_style_select" value="tssarrow"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2128 <section name="bed_advanced">
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2129 <param name="arrow_length" value="5000"/>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2130 </section>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2131 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2132 </conditional>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2133 </repeat>
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2134 <param name="image_file_format" value="png" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2135 <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="35000" />
326a3db8d9d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2" iuc parents: 6 diff changeset	2136 </test>
8 4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2137 <!--test 16-->
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2138 <test>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2139 <param name="region" value="X:2700000-3100000"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2140 <section name="global_args">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2141 <param name="decreasingXAxis" value="true"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2142 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2143 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2144 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2145 <param name="track_file_style_selector" value="bigwig_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2146 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2147 <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2148 <param name="height_bigwig" value="7" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2149 <param name="color" value="#00b0f0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2150 <section name="reading_bw_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2151 <param name="number_of_bins" value="2000"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2152 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2153 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2154 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2155 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2156 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2157 <param name="track_file_style_selector" value="bigwig_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2158 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2159 <param name="title" value="" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2160 <param name="color" value="#ff0000" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2161 <param name="alpha" value="0.5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2162 <param name="summary_method" value="max" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2163 <section name="reading_bw_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2164 <param name="number_of_bins" value="300"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2165 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2166 <param name="overlay_select" value="share-y"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2167 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2168 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2169 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2170 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2171 <param name="track_file_style_selector" value="xaxis_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2172 <param name="xaxis_where" value="bottom" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2173 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2174 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2175 <param name="image_file_format" value="png" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2176 <output name="outFileName" file="test_alpha_dec.png" ftype="png" compare="sim_size" delta="35000" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2177 </test>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2178 <!--test 17-->
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2179 <test>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2180 <param name="region" value="chr2:73,800,000-75,744,000"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2181 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2182 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2183 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2184 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2185 <param name="title" value="bedgraph color = blue transform = no" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2186 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2187 <param name="color" value="blue" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2188 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2189 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2190 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2191 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2192 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2193 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2194 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2195 <param name="title" value="bedgraph color = blue transform = log" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2196 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2197 <param name="color" value="blue" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2198 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2199 <param name="transform_selector" value="log"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2200 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2201 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2202 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2203 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2204 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2205 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2206 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2207 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2208 <param name="title" value="bedgraph color = red transform = log min_value = 1" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2209 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2210 <param name="color" value="red" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2211 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2212 <param name="transform_selector" value="log"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2213 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2214 <param name="min_value" value="1" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2215 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2216 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2217 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2218 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2219 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2220 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2221 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2222 <param name="title" value="bedgraph color = green transform = log log_pseudocount = 2 min_value = 0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2223 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2224 <param name="color" value="green" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2225 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2226 <param name="transform_selector" value="log"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2227 <param name="log_pseudocount" value="2"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2228 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2229 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2230 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2231 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2232 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2233 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2234 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2235 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2236 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2237 <param name="title" value="bedgraph color = green operation = log(2+file) min_value = 0.7" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2238 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2239 <param name="color" value="green" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2240 <section name="op">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2241 <param name="operation" value="log(2+file)" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2242 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2243 <param name="min_value" value="0.7" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2244 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2245 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2246 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2247 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2248 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2249 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2250 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2251 <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2252 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2253 <param name="color" value="black" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2254 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2255 <param name="transform_selector" value="log2"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2256 <param name="log_pseudocount" value="1"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2257 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2258 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2259 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2260 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2261 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2262 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2263 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2264 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2265 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2266 <param name="title" value="bedgraph color = black operation = log2(1+file) min_value = 0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2267 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2268 <param name="color" value="black" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2269 <section name="op">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2270 <param name="operation" value="log2(1+file)" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2271 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2272 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2273 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2274 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2275 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2276 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2277 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2278 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2279 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2280 <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2281 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2282 <param name="color" value="black" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2283 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2284 <param name="transform_selector" value="log2"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2285 <param name="log_pseudocount" value="1"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2286 <param name="y_axis_values" value="original"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2287 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2288 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2289 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2290 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2291 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2292 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2293 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2294 <param name="track_file_style_selector" value="xaxis_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2295 <param name="xaxis_where" value="bottom" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2296 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2297 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2298 <param name="image_file_format" value="png" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2299 <output name="outFileName" file="test_log.png" ftype="png" compare="sim_size" delta="35000" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2300 </test>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2301 <!--test 18-->
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2302 <test>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2303 <param name="region" value="chrX:2700000-3100000"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2304 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2305 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2306 <param name="track_file_style_selector" value="xaxis_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2307 <param name="xaxis_where" value="top" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2308 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2309 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2310 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2311 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2312 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2313 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2314 <param name="title" value="file summary_method = mean number_of_bins=20" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2315 <param name="height_bedgraph" value="4" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2316 <param name="color" value="blue" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2317 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2318 <section name="reading_bdg_as_bw" >
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2319 <param name="summary_method" value="mean" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2320 <param name="number_of_bins" value="20" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2321 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2322 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2323 <param name="max_value" value="30" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2324 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2325 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2326 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2327 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2328 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2329 <param name="track_input_bedgraph" value="bedgraph2_X_2.5e6_3.5e6.bdg" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2330 <param name="title" value="second_file summary_method = mean" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2331 <param name="height_bedgraph" value="4" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2332 <param name="color" value="red" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2333 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2334 <section name="reading_bdg_as_bw" >
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2335 <param name="summary_method" value="mean" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2336 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2337 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2338 <param name="max_value" value="30" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2339 <param name="spacer_height" value="0.5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2340 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2341 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2342 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2343 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2344 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2345 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2346 <param name="title" value="operation = log1p(file) (no summary_method)" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2347 <param name="height_bedgraph" value="4" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2348 <param name="color" value="blue" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2349 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2350 <section name="op">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2351 <param name="operation" value="log1p(file)" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2352 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2353 <param name="spacer_height" value="0.5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2354 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2355 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2356 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2357 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2358 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2359 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2360 <param name="title" value="operation = file - second_file" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2361 <param name="height_bedgraph" value="8" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2362 <param name="color" value="blue" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2363 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2364 <conditional name="color_negative">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2365 <param name="color_negative_select" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2366 <param name="color" value="red" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2367 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2368 <section name="op">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2369 <param name="operation" value="file - second_file" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2370 <param name="second_file" value="bedgraph2_X_2.5e6_3.5e6.bdg" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2371 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2372 <param name="min_value" value="-30" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2373 <param name="max_value" value="30" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2374 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2375 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2376 <param name="image_file_format" value="png" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2377 <output name="outFileName" file="test_operation.png" ftype="png" compare="sim_size" delta="35000" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2378 </test>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2379 <!--test 19-->
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2380 <test>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2381 <param name="region" value="chr2:73,800,000-75,744,000"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2382 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2383 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2384 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2385 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2386 <param name="title" value="bedgraph color = blue transform = no" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2387 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2388 <param name="color" value="blue" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2389 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2390 <param name="grid" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2391 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2392 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2393 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2394 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2395 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2396 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2397 <param name="title" value="bedgraph color = blue transform = log" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2398 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2399 <param name="color" value="blue" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2400 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2401 <param name="transform_selector" value="log"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2402 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2403 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2404 <param name="grid" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2405 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2406 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2407 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2408 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2409 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2410 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2411 <param name="title" value="bedgraph color = red transform = log min_value = 1" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2412 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2413 <param name="color" value="red" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2414 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2415 <param name="transform_selector" value="log"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2416 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2417 <param name="min_value" value="1" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2418 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2419 <param name="grid" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2420 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2421 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2422 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2423 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2424 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2425 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2426 <param name="title" value="bedgraph color = green transform = log log_pseudocount = 2 min_value = 0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2427 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2428 <param name="color" value="green" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2429 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2430 <param name="transform_selector" value="log"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2431 <param name="log_pseudocount" value="2"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2432 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2433 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2434 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2435 <param name="grid" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2436 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2437 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2438 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2439 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2440 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2441 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2442 <param name="title" value="bedgraph color = green operation = log(2+file) min_value = 0.7" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2443 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2444 <param name="color" value="green" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2445 <section name="op">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2446 <param name="operation" value="log(2+file)" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2447 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2448 <param name="min_value" value="0.7" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2449 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2450 <param name="grid" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2451 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2452 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2453 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2454 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2455 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2456 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2457 <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2458 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2459 <param name="color" value="black" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2460 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2461 <param name="transform_selector" value="log2"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2462 <param name="log_pseudocount" value="1"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2463 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2464 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2465 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2466 <param name="grid" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2467 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2468 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2469 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2470 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2471 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2472 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2473 <param name="title" value="bedgraph color = black operation = log2(1+file) min_value = 0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2474 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2475 <param name="color" value="black" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2476 <section name="op">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2477 <param name="operation" value="log2(1+file)" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2478 </section>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2479 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2480 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2481 <param name="grid" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2482 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2483 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2484 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2485 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2486 <param name="track_file_style_selector" value="bedgraph_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2487 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2488 <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2489 <param name="height_bedgraph" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2490 <param name="color" value="black" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2491 <conditional name="logScale_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2492 <param name="transform_selector" value="log2"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2493 <param name="log_pseudocount" value="1"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2494 <param name="y_axis_values" value="original"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2495 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2496 <param name="min_value" value="0" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2497 <param name="show_data" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2498 <param name="grid" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2499 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2500 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2501 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2502 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2503 <param name="track_file_style_selector" value="xaxis_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2504 <param name="xaxis_where" value="bottom" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2505 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2506 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2507 <param name="image_file_format" value="png" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2508 <output name="outFileName" file="test_log_grid.png" ftype="png" compare="sim_size" delta="35000" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2509 </test>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2510 <!--test 20-->
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2511 <test>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2512 <param name="region" value="chrX:3000000-3300000"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2513 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2514 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2515 <param name="track_file_style_selector" value="xaxis_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2516 <param name="xaxis_where" value="top" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2517 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2518 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2519 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2520 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2521 <param name="track_file_style_selector" value="spacer_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2522 <param name="spacer_height" value="0.05" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2523 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2524 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2525 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2526 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2527 <param name="track_file_style_selector" value="hic_matrix_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2528 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2529 <param name="title" value="depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops)" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2530 <param name="depth" value="300000" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2531 <param name="transform" value="log1p" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2532 <param name="min_value" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2533 <param name="show_masked_bins" value="false" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2534 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2535 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2536 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2537 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2538 <param name="track_file_style_selector" value="link_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2539 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2540 <conditional name="color_link">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2541 <param name="color" value="red" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2542 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2543 <param name="line_width" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2544 <param name="links_type" value="loops" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2545 <param name="overlay_select" value="share-y" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2546 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2547 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2548 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2549 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2550 <param name="track_file_style_selector" value="link_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2551 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2552 <conditional name="color_link">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2553 <param name="color" value="RdYlGn" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2554 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2555 <param name="line_width" value="3" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2556 <param name="invert_orientation" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2557 <param name="title" value="links line_width = 3 color RdYlGn" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2558 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2559 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2560 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2561 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2562 <param name="track_file_style_selector" value="spacer_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2563 <param name="spacer_height" value="1" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2564 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2565 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2566 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2567 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2568 <param name="track_file_style_selector" value="hic_matrix_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2569 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2570 <param name="title" value="depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops)" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2571 <param name="depth" value="300000" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2572 <param name="transform" value="log1p" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2573 <param name="min_value" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2574 <param name="show_masked_bins" value="false" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2575 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2576 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2577 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2578 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2579 <param name="track_file_style_selector" value="link_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2580 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2581 <conditional name="color_link">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2582 <param name="color" value="red" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2583 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2584 <param name="line_width" value="5" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2585 <param name="links_type" value="loops" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2586 <param name="overlay_select" value="share-y" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2587 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2588 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2589 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2590 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2591 <param name="track_file_style_selector" value="link_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2592 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2593 <conditional name="color_link">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2594 <param name="color" value="RdYlGn" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2595 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2596 <param name="line_width" value="3" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2597 <param name="invert_orientation" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2598 <param name="use_middle" value="true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2599 <param name="title" value="links line_width = 3 color RdYlGn use_middle = true" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2600 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2601 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2602 <repeat name="tracks">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2603 <conditional name="track_file_style_conditional">
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2604 <param name="track_file_style_selector" value="vlines_track_option" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2605 <param name="track_input_bed_single" value="tad_classification.bed" ftype="bed" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2606 <param name="line_width" value="3" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2607 </conditional>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2608 </repeat>
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2609 <param name="image_file_format" value="png" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2610 <output name="outFileName" file="test_arcs_use_middle.png" ftype="png" compare="sim_size" delta="35000" />
4ac4e7083b7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14" iuc parents: 7 diff changeset	2611 </test>
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2612 </tests>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2613 <help><![CDATA[
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2614
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2615 pyGenomeTracks
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2616 ==============
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2617
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	2618 pyGenomeTracks is a visualization tool which aims to produce high-quality genome browser tracks that are highly customizable.
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	2619 Currently, it is possible to plot:
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2620
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2621 - bigwig
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2622 - bed (many options)
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2623 - bedgraph
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2624 - links (represented as arcs)
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2625 - Hi-C matrices
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2626
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2627 _________________
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2628
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2629 Usage
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2630 -----
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2631
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2632 This tool takes various types of tracks as input:
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2633
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2634 - Chromatin states: display blocks of different colors following a bed file.
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2635 - Gene track / Bed Track: display genes or bed files. Labels like gene names can be toggled on or off.
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2636 - Bigwig track: generic bigwig track plotting.
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2637 - Bedgraph track: generic bedgraph track plotting.
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2638 - Bedgraph matrix track is used to specifically plot bm files computed by HiCExplorer's ``hicFindTADs`` (TAD seperation scores).
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2639 - Vlines: vertical lines drawn on top of all tracks following a bed file. It is used as a visual support where regions start / end over all tracks, for example to display TAD boundaries computed by HiCExplorer's ``hicFindTADs``.
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2640 - Spacer: Add some space between two tracks.
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2641 - Hi-C tracks:
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2642 - TAD vizualisation: corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow HiCExplorer's ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of HiCExplorer's ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap.
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2643 - TAD score: display TAD seperation score computed by HiCExplorer's ``hicFindTADs``.
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2644
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2645
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2646 For each track, parameters for the color, the width or the font size can be defined.
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2647
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2648 _________________
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2649
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2650 Output
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2651 ------
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2652
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	2653 pyGenomeTracks output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files)
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2654 also contains Hi-C data. The plot is composed of tracks that need to be specified.
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2655 Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using pyGenomeTracks.
2 c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	2656 TADs were computed by HiCExplorer's ``hicFindTADs``. The additional tracks added correspond to:
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	2657 TAD-separation score (as reported by HiCExplorer's ``hicFindTADs``), chromatin states,
c171f2b7d76e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e" iuc parents: 1 diff changeset	2658 principal component 1 (A/B compartment) computed using HiCExplorer's ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track.
0 2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2659 Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_.
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2660
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2661 .. image:: $PATH_TO_IMAGES/pyGenomeTracks.png
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2662 :width: 70 %
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2663
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2664 _________________
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2665
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2666 \| For more information about pyGenomeTracks please consider our documentation on github_
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2667
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2668 .. _github: https://github.com/deeptools/pyGenomeTracks
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2669 .. _`Nothjunge et al. (2017)`: https://www.nature.com/articles/s41467-017-01724-9
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2670 ]]></help>
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2671 <expand macro="citations" />
2074627b0f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363 iuc parents: diff changeset	2672 </tool>

Mercurial > repos > iuc > pygenometracks

annotate pyGenomeTracks.xml @ 8:4ac4e7083b7e draft