Mercurial > repos > bzeitouni > svdetect
diff svdetect/circos_graph.xml @ 28:091714bd75a0 draft default tip
new release r0.8b
| author | bzeitouni |
|---|---|
| date | Tue, 22 Jan 2013 06:20:22 -0500 |
| parents | c284618dd8da |
| children |
line wrap: on
line diff
--- a/svdetect/circos_graph.xml Tue Nov 06 10:06:26 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,290 +0,0 @@ -<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"> - -<ideogram> - -<spacing> - -default = 5u -break = 1u - -axis_break_at_edge = yes -axis_break = yes -axis_break_style = 2 - -<break_style 1> -stroke_color = black -fill_color = blue -thickness = 0.25r -stroke_thickness = 2 -</break> - -<break_style 2> -stroke_color = black -stroke_thickness = 3p -thickness = 1.5r -</break> - -</spacing> - -## 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 - -</ideogram> - - </configfile> - - <configfile name="ticks_config_file"> - -show_ticks = yes -show_tick_labels = yes - -<ticks> -radius = dims(ideogram,radius_outer) -multiplier = 1e-6 - -<tick> -spacing = 0.5u -size = 2p -thickness = 2p -color = grey -show_label = no -label_size = 12p -label_offset = 0p -format = %.2f -</tick> - -<tick> -spacing = 1u -size = 3p -thickness = 2p -color = dgrey -show_label = no -label_size = 12p -label_offset = 0p -format = %.2f -</tick> - -<tick> -spacing = 5u -size = 5p -thickness = 2p -color = black -show_label = yes -label_size = 16p -label_offset = 0p -format = %d -</tick> - -<tick> -spacing = 10u -size = 8p -thickness = 2p -color = black -show_label = yes -label_size = 20p -label_offset = 5p -format = %d -</tick> -</ticks> - </configfile> - - - <configfile name="circos_config_file"> -<colors> -<<include etc/colors.conf>> -</colors> - -<fonts> -<<include etc/fonts.conf>> -</fonts> - -<<include $ideogram_config_file>> -<<include $ticks_config_file>> - -karyotype = $karyotype - -<image> -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 -</image> - -chromosomes_units= $chromosomes_units - -#if str($chromosomes)=="" -chromosomes_display_default = yes -#else -chromosomes_display_default = no -chromosomes = $chromosomes -#end if - -<links> - -z = 0 -radius = 0.95r -bezier_radius = 0.2r - -<link segdup> -show = yes -color = dgrey_a5 -thickness = 2 -file = $link_file -record_limit = 1000 -</link> - -</links> - - -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 (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of Circos. - - - </help> - -</tool>