--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/circos.conf	Mon Feb 10 09:06:15 2014 -0500
@@ -0,0 +1,112 @@
+<image>
+png = yes
+dir = /home/users/kaufmann/Software/galaxy-dist/database/job_working_directory/000/230/dataset_329_files
+file = /home/users/kaufmann/Software/galaxy-dist/database/files/000/dataset_329.dat.png
+radius = 750p
+background=white
+image_map_use = yes
+image_map_name = circosmap
+angle_offset = -90
+auto_alpha_colors = yes
+auto_alpha_steps  = 5
+</image>
+karyotype = /home/users/kaufmann/Software/galaxy-dist/database/files/000/dataset_322.dat.karyotype
+chromosomes_units = 1000000
+chromosomes_display_default = no
+<colors>
+<<include /home/users/kaufmann/Software/shed-tools/testtoolshed.g2.bx.psu.edu/repos/s-kaufmann/synteny_mapper/036a03435919/synteny_mapper/circos-files/colors.synteny.conf>>
+<<include /home/users/kaufmann/Software/shed-tools/testtoolshed.g2.bx.psu.edu/repos/s-kaufmann/synteny_mapper/036a03435919/synteny_mapper/circos-files/colors.mouse.conf>>
+</colors>
+chromosomes = hs44542;mm44542
+chromosomes_reverse = mm44542
+<highlights>
+z = 5
+<highlight>
+file = /home/users/kaufmann/Software/galaxy-dist/database/files/000/dataset_321.dat.gene-track
+r0 = 0.9r
+r1 = 0.99r
+stroke_thickness = 1
+stroke_color = black
+</highlight>
+</highlights>
+<plots>
+<plot>
+type=text
+color=black
+file=/home/users/kaufmann/Software/galaxy-dist/database/files/000/dataset_321.dat.gene-track-labels
+r0=0.99r
+r1=1.5r
+label_size=9
+label_font=condensed
+show_links=yes
+link_dims = 0p,90p,20p,10p,20p
+link_thickness=1
+link_color=black
+padding =0p
+rpadding = 0p
+</plot>
+
+</plots>
+<links>
+<link>
+file = /home/users/kaufmann/Software/galaxy-dist/database/files/000/dataset_321.dat.links
+radius = 0.88r
+bezier_radius = 0r
+color = link_a4
+stroke_thickness = 1
+z = 10
+ribbon = yes
+<rules>
+<rule>
+condition = var(size1) < 10 || var(size2) < 10
+stroke_thickness = 5
+flow = continue
+</rule>
+<rule>
+condition = 1
+z = eval(scalar min(var(size1),var(size2)))
+flow = continue
+</rule>
+<rule>
+condition = 1
+stroke_color = link
+flow = continue
+</rule>
+<rule>
+condition = 1
+color = link_a4
+</rule>
+</rules>
+</link>
+<link>
+file = /home/users/kaufmann/Software/galaxy-dist/database/files/000/dataset_321.dat.jumped
+radius = 0.88r
+bezier_radius = 0r
+color = link_jumped_a4
+stroke_thickness = 1
+z = 10
+ribbon = yes
+<rules>
+<rule>
+condition = var(size1) < 10 || var(size2) < 10
+stroke_thickness = 5
+flow = continue
+</rule>
+<rule>
+condition = 1
+z = eval(scalar min(var(size1),var(size2)))
+flow = continue
+</rule>
+<rule>
+condition = 1
+stroke_color = link_jumped
+flow = continue
+</rule>
+<rule>
+condition = 1
+color = link_jumped_a4
+</rule>
+</rules>
+</link>
+</links>
+<<include /home/users/kaufmann/Software/shed-tools/testtoolshed.g2.bx.psu.edu/repos/s-kaufmann/synteny_mapper/036a03435919/synteny_mapper/circos-files/synteny-region-default.conf>>