Mercurial > repos > bzeitouni > svdetect
view 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 |
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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"> <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>