annotate gv/svdetect/circos_graph.xml @ 15:17c5d1e6f09b draft

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<tool id="circos_graph" name="Circos" version="1.1.0">

<description>plots</description>

<command interpreter="perl">circos/bin/circos

-conf '$circos_config_file'
-outputfile '${outputfile}.dat'
-png 

> '$log_file'

;

rm '$outputfile'; ln -s '${outputfile}.png' '$outputfile' 

</command>


<inputs>
	<param name="graph_name" type="text" size="20" value="graph1" label="Graph name"/>
	
	<param name="karyotype" type="select" format="txt" label="Type of model organism">
		<option value="data/karyotype.human_hg19.txt">Human (homo sapiens, hs) -hg19-</option>
		<option value="data/karyotype.human.txt">Human (homo sapiens, hs) -hg18-</option>
		<option value="data/2/karyotype.mouse.txt">Mouse (Mus Musculus, mm)</option>
		<option value="data/2/karyotype.dog.txt">Dog (Canis familiaris, cf)</option>
		<option value="data/2/karyotype.rt.txt">Rat (Rattus norvegicus, rn)</option>
		<option value="data/karyotype.yeast.txt">Yeast (Saccharomyces Cerevisiae, sc) -SGD-</option>

  	</param>
	<param name="chromosomes_units" type="integer" size="50" value="1000000" label="Chromosomes units"/>
	<param name="chromosomes" type="text" size="100" value="" label="List of chromosome names to keep or exclude" help="ex: hs2;hs3 or -hsX;-hsY">
		<sanitizer>
			<valid initial="string.printable">
				<add value=";"/>
			</valid>
		</sanitizer>
	</param>
	<param name="link_file" format="segdup" type="data" label="Input link file (.segdup)"/>
</inputs>

<outputs>
	<data format="txt" name="log_file" label="${graph_name}.circos.log"/>
	<data format="png" name="outputfile" label="${graph_name}.png"/>
</outputs>



<configfiles>
	<configfile name="ideogram_config_file">
		
&lt;ideogram&gt;

&lt;spacing&gt;

default = 5u
break   = 1u

axis_break_at_edge = yes
axis_break         = yes
axis_break_style   = 2

&lt;break_style 1&gt;
stroke_color = black
fill_color   = blue
thickness    = 0.25r
stroke_thickness = 2
&lt;/break&gt;

&lt;break_style 2&gt;
stroke_color     = black
stroke_thickness = 3p
thickness        = 1.5r
&lt;/break&gt;

&lt;/spacing&gt;

## thickness (px) of chromosome ideogram
thickness        = 100p
stroke_thickness = 2
## ideogram border color
stroke_color     = black
fill             = yes
## the default chromosome color is set here and any value
## defined in the karyotype file overrides it
fill_color       = black

## fractional radius position of chromosome ideogram within image
radius         = 0.85r
show_label     = yes
label_with_tag = yes
label_font     = condensedbold
label_radius   = dims(ideogram,radius) + 0.075r
label_size     = 60p

## cytogenetic bands
band_stroke_thickness = 2

## show_bands determines whether the outline of cytogenetic bands
## will be seen
show_bands            = yes
## in order to fill the bands with the color defined in the karyotype
## file you must set fill_bands
fill_bands            = yes

&lt;/ideogram&gt;

	</configfile>

	<configfile name="ticks_config_file">
	
show_ticks          = yes
show_tick_labels    = yes

&lt;ticks&gt;
radius               = dims(ideogram,radius_outer)
multiplier           = 1e-6

&lt;tick&gt;
spacing        = 0.5u
size           = 2p
thickness      = 2p
color          = grey
show_label     = no
label_size     = 12p
label_offset   = 0p
format         = %.2f
&lt;/tick&gt;
	
&lt;tick&gt;
spacing        = 1u
size           = 3p
thickness      = 2p
color          = dgrey
show_label     = no
label_size     = 12p
label_offset   = 0p
format         = %.2f
&lt;/tick&gt;

&lt;tick&gt;
spacing        = 5u
size           = 5p
thickness      = 2p
color          = black
show_label     = yes
label_size     = 16p
label_offset   = 0p
format         = %d
&lt;/tick&gt;

&lt;tick&gt;
spacing        = 10u
size           = 8p
thickness      = 2p
color          = black
show_label     = yes
label_size     = 20p
label_offset   = 5p
format         = %d
&lt;/tick&gt;
&lt;/ticks&gt;
	</configfile>	
	
	
	<configfile name="circos_config_file">
&lt;colors&gt;
&lt;&lt;include etc/colors.conf&gt;&gt;
&lt;/colors&gt;

&lt;fonts&gt;
&lt;&lt;include etc/fonts.conf&gt;&gt;
&lt;/fonts&gt;

&lt;&lt;include $ideogram_config_file&gt;&gt;
&lt;&lt;include $ticks_config_file&gt;&gt;

karyotype = $karyotype

&lt;image&gt;
24bit = yes
##png = yes
##svg = no
## radius of inscribed circle in image
radius         = 1500p
background     = white
## by default angle=0 is at 3 o'clock position
angle_offset   = -90
#angle_orientation = counterclockwise

auto_alpha_colors = yes
auto_alpha_steps  = 5
&lt;/image&gt;

chromosomes_units= $chromosomes_units

#if str($chromosomes)==""
chromosomes_display_default = yes
#else
chromosomes_display_default = no
chromosomes = $chromosomes
#end if

&lt;links&gt;

z      = 0
radius = 0.95r
bezier_radius = 0.2r

&lt;link segdup&gt;
show         = yes
color        = dgrey_a5
thickness    = 2
file         = $link_file
record_limit = 1000
&lt;/link&gt;

&lt;/links&gt;


anglestep       = 0.5
minslicestep    = 10
beziersamples   = 40
debug           = no
warnings        = no
imagemap        = no

units_ok = bupr
units_nounit = n
	</configfile>
</configfiles>

  <help>
**What it does**

Circos

Manual documentation available at the http://circos.ca/


**Example of link segdup file**

segdup file::

    1	hs1	1077096	1078746	color=red
    1	hs1	1080923	1082805	color=red
    2	hs1	1137684	1137961	color=red
    2	hs3	1138138	1138423	color=red
    3	hs11	1169417	1170000	color=red
    3	hs11	1170025	1170975	color=red
    4	hs11	1222480	1224271	color=green
    4	hs11	1223328	1225675	color=green
    5	hs12	1223336	1225812	color=grey
    5	hs13	1224709	1227633	color=grey
    6	hs11	1223621	1226460	color=red
    6	hs11	1224918	1227633	color=red
    7	hs11	1399510	1401513	color=white
    7	hs11	1401628	1403697	color=white
    8	hs15	1652045	1653746	color=red
    8	hs15	1657167	1658940	color=red
    9	hs11	165333	165887	color=white
    9	hs11	165981	168016	color=white
    10	hs11	1702700	1702841	color=red
    10	hs11	1702903	1703057	color=red
    11	hs11	1912272	1915186	color=white
    11	hs11	1937111	1939824	color=white
    12	hs11	1983211	1983355	color=red
    12	hs11	1983591	1983748	color=red
    13	hs11	2913657	2913898	color=white
    13	hs11	2914048	2914341	color=white
    14	hs11	3090593	3090749	color=purple
    14	hs11	3090709	3090864	color=purple
    15	hs21	3466365	3466434	color=red
    15	hs21	3466554	3466620	color=red
    16	hsX	3603073	3603321	color=white
    16	hsX	3603295	3603520	color=white


    
-----

.. class:: infomark

Contact Bruno Zeitouni ([e-mail]) for any questions or concerns about the Galaxy implementation of Circos.
    
    
  </help>

</tool>