Mercurial > repos > bzeitouni > svdetect
diff SVDetect_r0.8b_galaxy/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 | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SVDetect_r0.8b_galaxy/svdetect/circos_graph.xml Tue Jan 22 06:20:22 2013 -0500 @@ -0,0 +1,290 @@ +<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>