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macros_conffiles.xml
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macros_conffiles.xml
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<?xml version="1.0"?>
<macros>
<xml name="configfile_circos_conf">
<configfile name="circos_conf"><![CDATA[
<<include colors_fonts_patterns.conf>>
<<include housekeeping.conf>>
karyotype = karyotype.txt
<image>
<<include etc/image.conf>>
</image>
<<include ticks.conf>>
<<include ideogram.conf>>
<plots>
<<include 2d.conf>>
<<include plot_highlight.conf>>
</plots>
<links>
<<include links.conf>>
</links>
<<include highlight.conf>>
]]></configfile>
</xml>
<xml name="configfile_ticks_conf">
<configfile name="ticks_conf"><![CDATA[
show_ticks = ${ticks.show_ticks}
show_tick_labels = yes
#def circosColor($value)
#set $value = str($value)
#set $r = int($value[1:3], 16)
#set $g = int($value[3:5], 16)
#set $b = int($value[5:], 16)
$r, $g, $b
#end def
<ticks>
radius = ${ticks.radius}r
color = $circosColor($ticks.color)
thickness = 2p
multiplier = ${ticks.multiplier}
#for $tick_group in $ticks.tick_group:
<tick>
spacing = ${tick_group.spacing}
size = ${tick_group.size}p
show_label = ${tick_group.show_tick_labels}
label_size = ${tick_group.label_size}p
label_offset = ${tick_group.label_offset}p
format = ${tick_group.format} kb
## TODO: figure out automated tick labels
##if ${ticks.multiplier} * ${tick_group.spacing}
</tick>
#end for
</ticks>
]]>
</configfile>
</xml>
<xml name="configfile_ideogram_conf">
<configfile name="ideogram_conf"><![CDATA[
<ideogram>
<spacing>
## spacing between ideograms
default = ${ideogram.spacing}r
</spacing>
# ideogram position, thickness and fill
radius = ${ideogram.radius}r
thickness = ${ideogram.thickness}p
fill = yes
show_label = ${ideogram.ideogram_labels.show_label}
label_radius = dims(ideogram,radius) + 0.075r
label_size = 24
label_parallel = ${ideogram.ideogram_labels.parallel}
show_bands = yes
fill_bands = yes
band_transparency = 4
</ideogram>
]]></configfile>
</xml>
<xml name="configfile_data_conf">
<configfile name="data_conf"><![CDATA[
#for $hi, $data in enumerate($sec_tdd.data):
<plot>
#set plot_type = str($data.plot_format.plot_format_select)
#def circosColor($value)
#set $value = str($value)
#set $r = int($value[1:3], 16)
#set $g = int($value[3:5], 16)
#set $b = int($value[5:], 16)
$r, $g, $b
#end def
type = ${plot_type}
file = data/data-${hi}.txt
r1 = ${data.r1}r
r0 = ${data.r0}r
orientation = ${data.orientation}
#if str($plot_type) == 'histogram':
extend_bin = ${data.plot_format.format_specific.extend_bins}
fill_color = ${data.plot_format.format_specific.fill_color}
#else if str($plot_type) == 'heatmap':
color = $circosColor($data.plot_format.format_specific.fill_color)
scale_log_base = ${data.plot_format.format_specific.scale_log_base}
#else if str($plot_type) == 'line':
color = $circosColor($data.plot_format.format_specific.color)
thickness = ${data.plot_format.format_specific.thickness}
#else if str($plot_type) == 'scatter':
glyph = ${data.plot_format.format_specific.glyph}
glyph_size = ${data.plot_format.format_specific.glyph_size}
color = $circosColor($data.plot_format.format_specific.color)
stroke_color = $circosColor($data.plot_format.format_specific.stroke_color)
stroke_thickness = ${data.plot_format.format_specific.stroke_thickness}
#else if str($plot_type) == 'tile':
color = ${data.plot_format.format_specific.color}
stroke_color = $circosColor($data.plot_format.format_specific.color)
stroke_thickness = ${data.plot_format.format_specific.stroke_thickness}
layers = ${data.plot_format.format_specific.layers}
thickness = ${data.plot_format.format_specific.thickness}
padding = ${data.plot_format.format_specific.padding}
layers_overflow = ${data.plot_format.format_specific.overflow.overflow_behavior}
#if str($data.plot_format.format_specific.overflow.overflow_behavior) != "hide":
layers_overflow_color = $circosColor($data.plot_format.format_specific.overflow.layer_overflow_color)
#end if
#end if
<rules>
#for $rule in $data.sec_rule.rules:
<rule>
#for $condition in $rule.conditions
#if str($condition.application.application_select) == "1":
condition = 1
#elif str($condition.application.application_select) == "on":
#set on_str = ' '.join([ "on(%s)" % $chr.strip() for $chr in $condition.application.on_genomes.split(',') ])
condition = $on_str
#elif str($condition.application.application_select) == "pos":
#if float($condition.application.pos_gt) != 0:
condition = var(start) > $condition.application.pos_gt
#end if
#if float($condition.application.pos_lt) != 0:
condition = var(start) < $condition.application.pos_lt
#end if
#elif str($condition.application.application_select) == "value":
#if float($condition.application.pos_gt) != 0:
condition = var(value) > $condition.application.pos_gt
#end if
#if float($condition.application.pos_lt) != 0:
condition = var(value) < $condition.application.pos_lt
#end if
#elif str($condition.application.application_select) == "var":
condition = var(${condition.application.varname}) ${condition.application.cond_select} "${condition.application.varvalue}"
#end if
#end for
#for $action in $rule.actions:
#if str($action.action.action_select) == "fill_color_value" or str($action.action.action_select) == "color_value" :
#set x_fill_color = $action.action.action_value
#set x_fill_color_count = int(str($x_fill_color).split('-')[1])
#set x_min = $x_fill_color_count if $action.action.invert else 1
#set x_max = 1 if $action.action.invert else $x_fill_color_count
#set color_action = "fill_color" if str($plot_type) == 'histogram' else "color"
$color_action = eval(sprintf("${action.action.action_value}-%d", remap_int(var(value), ${action.action.min_value}, ${action.action.max_value}, ${x_min}, ${x_max})))
#else
$action.action.action_select = ${action.action.action_value}
#end if
#end for
$rule.continue_flow
</rule>
#end for
</rules>
<axes>
#for $axis in $data.sec_axes.axes:
<axis>
color = $circosColor($axis.color)
thickness = ${axis.thickness}
spacing = ${axis.spacing}r
y0 = ${axis.y0}r
y1 = ${axis.y1}r
</axis>
#end for
</axes>
<backgrounds>
#for $bkg in $data.sec_bkgs.backgrounds:
<background>
color = $circosColor($bkg.color)
y0 = ${bkg.y0}r
y1 = ${bkg.y1}r
</background>
#end for
</backgrounds>
</plot>
#end for
]]></configfile>
</xml>
<xml name="configfile_links_conf">
<configfile name="links_conf"><![CDATA[
#for $hi, $data in enumerate($sec_links.data):
<link>
#def circosColor($value)
#set $value = str($value)
#set $r = int($value[1:3], 16)
#set $g = int($value[3:5], 16)
#set $b = int($value[5:], 16)
$r, $g, $b
#end def
file = data/links-${hi}.txt
radius = ${data.radius}r
ribbon = ${data.linktype.ribbon}
#if $data.linktype.ribbon == 'yes'
${data.linktype.twist}
#end if
color = $circosColor($data.color)
bezier_radius = ${data.bezier_radius}r
thickness = ${data.thickness}
crest = ${data.advanced.crest}
bezier_radius_purity = ${data.advanced.bezier_radius_purity}
#if $data.advanced.perturbation.perturb == 'yes'
perturb = yes
perturb_crest = ${data.advanced.perturbation.perturb_crest_min},${data.advanced.perturbation.perturb_crest_max}
perturb_bezier_radius = ${data.advanced.perturbation.perturb_bezier_radius_min},${data.advanced.perturbation.perturb_bezier_radius_max}
perturb_bezier_radius_purity = ${data.advanced.perturbation.perturb_bezier_radius_purity_min},${data.advanced.perturbation.perturb_bezier_radius_purity_max}
#end if
#if $data.advanced.zdepth
z = ${data.advanced.zdepth}
#end if
<rules>
#for $rule in $data.sec_link_rule.rules:
<rule>
#for $condition in $rule.conditions
#set cond = $condition.application.application_select
#if $cond == 'interchr' or $cond == 'intrachr' or $cond == 'inv' or $cond == 'rev'
condition = var($cond)
#elif $cond == 'always'
condition = 1
#else
#set op = $condition.application.comparison.compare
#set val = $condition.application.comparison.compval
#if $cond == 'chr'
#if $op == 'between' or $op == 'fromto'
#set val2 = $condition.application.comparison.compval2
#set c=''.join([str($op),"(",str($val),",",str($val2),")"])
#else
#set c=''.join([str($op),"(",str($val),")"])
#end if
condition = $c
#else
#if $cond == 'dist' and $op == 'lt'
condition = abs(var(pos1) - var(pos2)) < $val
#elif $cond == 'dist' and $op == 'gt'
condition = abs(var(pos1) - var(pos2)) > $val
#elif $op == 'lt'
condition = var($cond) < $val
#elif $op == 'gt'
condition = var($cond) > $val
#end if
#end if
#end if
#end for
#for $action in $rule.actions:
#set actiontype = $action.action.action_select
#if $actiontype == 'color':
#if $action.action.dynamic.dynamic_select == "static":
#set actionval = $circosColor($action.action.dynamic.action_value)
$actiontype = $actionval
#else
#set x_fill_color = $action.action.dynamic.action_value
#set x_fill_color_count = int(str($x_fill_color).split('-')[1])
#set x_min = $x_fill_color_count if $action.action.dynamic.invert else 1
#set x_max = 1 if $action.action.dynamic.invert else $x_fill_color_count
$actiontype = eval(sprintf("${action.action.dynamic.action_value}-%d", remap_int(var(value), ${action.action.dynamic.min_value}, ${action.action.dynamic.max_value}, ${x_min}, ${x_max})))
#end if
#elif $actiontype == 'z':
#if $action.action.dynamic.dynamic_select == "static":
#set actionval = $action.action.dynamic.action_value
$actiontype = $actionval
#else
#set x_min = 1000 if $action.action.dynamic.invert else 1
#set x_max = 1 if $action.action.dynamic.invert else 1000
$actiontype = eval(remap_int(var(value), ${action.action.dynamic.min_value}, ${action.action.dynamic.max_value}, ${x_min}, ${x_max}))
#end if
#else
#set actionval = $action.action.action_value
$actiontype = $actionval
#end if
#end for
$rule.continue_flow
</rule>
#end for
</rules>
</link>
#end for
]]></configfile>
</xml>
<xml name="configfile_plot_highlight_conf">
<configfile name="plot_highlight_conf"><![CDATA[
###for $hi, $highlight in enumerate($sec_heat.highlights):
## #if $highlight.type_select == "plot_highlights":
##<plot>
## type = highlight
## file = data/highlight-${hi}.txt
## r1 = ${highlight.r1}r
## r0 = ${highlight.r0}r
## color = ${highlight.fill_color}
##</plot>
## #end if
###end for
]]></configfile>
</xml>
<xml name="configfile_highlight_conf">
<configfile name="highlight_conf"><![CDATA[
##<highlights>
###for $hi, $highlight in enumerate($sec_heat.highlights):
## #if $highlight.type_select == "normal":
## <highlight>
## file = data/highlight-${hi}.txt
## r1 = ${highlight.r1}r
## r0 = ${highlight.r0}r
## color = ${highlight.fill_color}
## </highlight>
## #end if
###end for
##</highlights>
]]></configfile>
</xml>
<xml name="test_case">
<configfile name="test_case_conf"><![CDATA[
<!--
mkdir -p test-data/my-test-case/;
#if $reference_genome.reference_genome_source == 'history':
cp ${genome_fasta} test-data/my-test-case/input.fa;
#end if
#if $reference_genome.reference_genome_source != 'karyotype':
#if $reference_genome.bands:
cp ${reference_genome.bands} test-data/my-test-case/bands.${reference_genome.bands.ext};
#end if
#end if
#for $idx, $data in enumerate($sec_tdd.data):
#if str($data.plot_format.plot_format_select) in ('histogram', 'heatmap'):
#for $jdx, $file in enumerate($data.plot_format.data_source):
cp ${file} test-data/my-test-case/${idx}-${jdx}.${file.ext};
#end for
#else
cp ${data.plot_format.data_source} test-data/my-test-case/${idx}.${data.plot_format.data_source.ext};
#end if
#end for
cp "$output_png" test-data/my-test-case/output.png;
cp "$output_svg" test-data/my-test-case/output.svg;
-->
<test>
<param name="reference_genome|reference_genome_source" value="${reference_genome.reference_genome_source}"/>
<param name="reference_genome|genome_fasta" value="my-test-case/input.fa" />
<!-- ideograms -->
<param name="ideogram|spacing" value="${ideogram.spacing}" />
<param name="ideogram|radius" value="${ideogram.radius}" />
<param name="ideogram|thickness" value="${ideogram.thickness}" />
<param name="ideogram|ideogram_labels|show_label" value="${ideogram.ideogram_labels.show_label}" />
<param name="ideogram|ideogram_labels|parallel" value="${ideogram.ideogram_labels.parallel}" />
#if $reference_genome.reference_genome_source != 'karyotype':
#if $reference_genome.bands:
<param name="reference_genome.bands" value="my-test-case/bands.${reference_genome.bands.ext}" />
#end if
#end if
<!-- Ticks -->
<param name="ticks|show_ticks" value="${ticks.show_ticks}" />
<param name="ticks|radius" value="${ticks.radius}" />
<param name="ticks|color" value="${ticks.color}" />
<param name="ticks|multiplier" value="${ticks.multiplier}" />
#for $idx, $tick_group in enumerate($ticks.tick_group):
<param name="ticks|tick_group_${idx}|tickspacing" value="${tick_group.spacing}" />
<param name="ticks|tick_group_${idx}|size" value="${tick_group.size}" />
<param name="ticks|tick_group_${idx}|show_tick_labels" value="${tick_group.show_tick_labels}" />
<param name="ticks|tick_group_${idx}|label_size" value="${tick_group.label_size}" />
<param name="ticks|tick_group_${idx}|label_offset" value="${tick_group.label_offset}" />
<param name="ticks|tick_group_${idx}|label_format" value="${tick_group.format}" />
#end for
<!-- Data -->
#for $idx, $data_group in enumerate($sec_tdd.data):
<param name="sec_tdd|data_${idx}|r0" value="${data_group.r0}" />
<param name="sec_tdd|data_${idx}|r1" value="${data_group.r1}" />
<param name="sec_tdd|data_${idx}|orientation" value="${data_group.orientation}" />
<param name="sec_tdd|data_${idx}|plot_format|plot_format_select" value="${data_group.plot_format.plot_format_select}" />
<!-- Note, please double check your files -->
#if str($data_group.plot_format.plot_format_select) == 'histogram':
#set my_files = ','.join([ "my-test-case/%s-%s.%s" % ($idx, $j, $file.ext) for ($j, $file) in enumerate($data_group.plot_format.data_source)])
<param name="sec_tdd|data_${idx}|plot_format|data_source" value="${my_files}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|fill_color" value="${data_group.plot_format.format_specific.fill_color}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|extend_bins" value="${data_group.plot_format.format_specific.extend_bins}" />
#else if str($data_group.plot_format.plot_format_select) == 'heatmap':
#set my_files = ','.join([ "my-test-case/%s-%s.%s" % ($idx, $j, $file.ext) for ($j, $file) in enumerate($data_group.plot_format.data_source)])
<param name="sec_tdd|data_${idx}|plot_format|data_source" value="${my_files}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|fill_color" value="${data_group.plot_format.format_specific.fill_color}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|scale_log_base" value="${data_group.plot_format.format_specific.scale_log_base}" />
#else if str($data_group.plot_format.plot_format_select) == 'line':
<param name="sec_tdd|data_${idx}|plot_format|data_source" value="my-test-case/${idx}.${data.plot_format.data_source.ext}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|color" value="${data_group.plot_format.format_specific.color}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke" value="${data_group.plot_format.format_specific.stroke}" />
#else if str($data_group.plot_format.plot_format_select) == 'scatter':
<param name="sec_tdd|data_${idx}|plot_format|data_source" value="my-test-case/${idx}.${data.plot_format.data_source.ext}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|glyph" value="${data_group.plot_format.format_specific.glyph}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|glyph_size" value="${data_group.plot_format.format_specific.glyph_size}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|data_min" value="${data_group.plot_format.format_specific.data_min}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|data_max" value="${data_group.plot_format.format_specific.data_max}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|color" value="${data_group.plot_format.format_specific.color}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke_color" value="${data_group.plot_format.format_specific.stroke_color}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke_thickness" value="${data_group.plot_format.format_specific.stroke_thickness}" />
#else if str($data_group.plot_format.plot_format_select) == 'tile':
<param name="sec_tdd|data_${idx}|plot_format|data_source" value="my-test-case/${idx}.${data.plot_format.data_source.ext}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|fill_color" value="${data_group.plot_format.format_specific.fill_color}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|color" value="${data_group.plot_format.format_specific.color}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke_thickness" value="${data_group.plot_format.format_specific.stroke_thickness}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|layers" value="${data_group.plot_format.format_specific.layers}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|thickness" value="${data_group.plot_format.format_specific.thickness}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|padding" value="${data_group.plot_format.format_specific.padding}" />
<param name="sec_tdd|data_${idx}|plot_format|format_specific|overflow|overflow_behavior" value="${data_group.plot_format.format_specific.overflow.overflow_behavior}" />
#if str($data_group.plot_format.format_specific.overflow.overflow_behavior) != 'hide':
<param name="sec_tdd|data_${idx}|plot_format|format_specific|overflow|layer_overflow_color" value="${data_group.plot_format.format_specific.overflow.layer_overflow_color}" />
#end if
#end if
## Next line intentionally blank
#end for
<!-- Outputs -->
<output name="output_png" file="my-test-case/output.png" />
<output name="output_svg" file="my-test-case/output.svg" />
</test>
]]></configfile>
</xml>
</macros>