Mercurial > repos > bornea > apostl_static_bubblegraph_generator
changeset 26:ed4d14e83f44 draft
Uploaded
| author | bornea |
|---|---|
| date | Wed, 18 May 2016 16:56:23 -0400 |
| parents | f0901a52b310 |
| children | 33e9cdd6bbe8 |
| files | APOSTL_Static_Bubblegraph_Generator.xml |
| diffstat | 1 files changed, 70 insertions(+), 1472 deletions(-) [+] |
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--- a/APOSTL_Static_Bubblegraph_Generator.xml Tue May 17 13:00:42 2016 -0400 +++ b/APOSTL_Static_Bubblegraph_Generator.xml Wed May 18 16:56:23 2016 -0400 @@ -1,1429 +1,34 @@ <tool id="APOSTL_Static_Bubblegraph_Generator" name="APOSTL Static Bubblegraph Generator"> <description></description> - <command interpreter="python">APOSTL_Static_Bubblegraph_Generator.py $list_file $prey_file $crapome $inter $main_x $main_y $size_id $color $SS_cutoff $FC_cutoff $NS_cutoff $theme $label $label_color $bubble_color $outline_color $filt_color $outfile \$INSTALL_RUN_PATH/ - </command> - <requirements> - <requirement type="set_environment">INSTALL_RUN_PATH</requirement> - </requirements> + <command interpreter="python">APOSTL_Static_Bubblegraph_Generator.py $list_file $prey_file $crapome $color $label $cutoff $type $inc_file $exc_file $outfile $NSAF_zoom $SAINT_zoom $SAINT $NSAF </command> <inputs> + <param type="select" name="type" label="MaxQuant or Scaffold"> + <option value="MQ">MaxQuant</option> + <option value="SC">Scaffold</option> + </param> <param format="txt" name="list_file" type="data" label="List File"/> <param format="txt" name="prey_file" type="data" label="Prey File"/> <param format="txt" name="crapome" type="data" label="Crapome File" optional="true"/> - <param format="txt" name="inter" type="data" label="Inter File"/> - <param name="main_x" type="select" label="X Axis" > - <option value="lnNSAF">ln(NSAF)</option> - <option value="SpecSum">SpecSum</option> - <option value="log2FoldChange">log2(FoldChange)</option> - <option value="SaintScore">SaintScore</option> - <option value="logOddsScore">logOddsScore</option> - <option value="NSAFScore">NSAFScore</option> - </param> - <param name="main_y" type="select" label="Y Axis" > - <option value="lnNSAF">ln(NSAF)</option> - <option value="SpecSum">SpecSum</option> - <option value="log2FoldChange">log2(FoldChange)</option> - <option value="SaintScore">SaintScore</option> - <option value="logOddsScore">logOddsScore</option> - <option value="NSAFScore">NSAFScore</option> - </param> - <param name="size_id" type="select" label="Bubble Size" > - <option value="fixed">fixed</option> - <option value="lnNSAF">ln(NSAF)</option> - <option value="SpecSum">SpecSum</option> - <option value="log2FoldChange">log2(FoldChange)</option> - <option value="SaintScore">SaintScore</option> - <option value="logOddsScore">logOddsScore</option> - <option value="NSAFScore">NSAFScore</option> - </param> - <param name="color" type="select" label="Color" > + <param name="color" type="select" label="Color" optional="true"> <option value="crapome">Crapome</option> - <option value="fixed">fixed</option> - </param> - <param type="float" name="SS_cutoff" label="SAINT Score Cutoff" help="Select a value between 0 and 1 written like 0.8." value="0.8"/> - <param type="integer" name="FC_cutoff" label="Fold Change Cutoff" help="Select a value between -Inf and Inf." value="0"/> - <param type="integer" name="NS_cutoff" label="NSAF Score Cutoff" help="Select a value between -Inf and Inf." value="0"/> - <param name="theme" type="select" label="Plot Theme" > - <option value="Default">Default</option> - <option value="b/w">b/w</option> - <option value="minimal">minimal</option> - <option value="classic">classic</option> - <option value="dark">dark</option> - <option value="linedraw">linedraw</option> - </param> - <param name="label" type="select" label="Label Type" > - <option value="none">none</option> - <option value="cutoff">cutoff</option> - <option value="all">all</option> - </param> - <param name="label_color" type="select" label="Label Color" > - <option value="black">Black</option> - <option value="white">White</option> + <option value="red">Red</option> + <option value="blue">Blue</option> </param> - <param name="bubble_color" type="select" label="Bubble Color" > - <option value="AirForceblue">AirForceblue</option> - <option value="Aliceblue">Aliceblue</option> - <option value="Alizarincrimson">Alizarincrimson</option> - <option value="Almond">Almond</option> - <option value="Amaranth">Amaranth</option> - <option value="Amber">Amber</option> - <option value="Americanrose">Americanrose</option> - <option value="Amethyst">Amethyst</option> - <option value="AndroidGreen">AndroidGreen</option> - <option value="AirForceblue">Antiflashwhite</option> - <option value="Antiquefuchsia">Antiquefuchsia</option> - <option value="Antiquewhite">Antiquewhite</option> - <option value="Ao">Ao</option> - <option value="Applegreen">Applegreen</option> - <option value="Apricot">Apricot</option> - <option value="Aqua">Aqua</option> - <option value="Amber">Amber</option> - <option value="Aquamarine">Aquamarine</option> - <option value="Amethyst">Amethyst</option> - <option value="Armygreen">Armygreen</option> - <option value="Arsenic">Arsenic</option> - <option value="Arylideyellow">Arylideyellow</option> - <option value="Ashgray">Ashgray</option> - <option value="Asparagus">Asparagus</option> - <option value="Atomictangerine">Atomictangerine</option> - <option value="Auburn">Auburn</option> - <option value="Aureolin">Aureolin</option> - <option value="AuroMetalSaurus">AuroMetalSaurus</option> - <option value="Awesome">Awesome</option> - <option value="Azuremist">Azuremist</option> - <option value="Babyblue">Babyblue</option> - <option value="Babypink">Babypink</option> - <option value="BallBlue">BallBlue</option> - <option value="BananaMania">BananaMania</option> - <option value="Bananayellow">Bananayellow</option> - <option value="Battleshipgray">Battleshipgray</option> - <option value="Bazaar">Bazaar</option> - <option value="Beaublue">Beaublue</option> - <option value="Beaver">Beaver</option> - <option value="Beige">Beige</option> - <option value="Bisque">Bisque</option> - <option value="Bistre">Bistre</option> - <option value="Bittersweet">Bittersweet</option> - <option value="Obsidian">Obsidian</option> - <option value="Onyx">Onyx</option> - <option value="LostSoul">LostSoul</option> - <option value="Midnight">Midnight</option> - <option value="RollingBlackout">RollingBlackout</option> - <option value="SleepingPanther">SleepingPanther</option> - <option value="VoidbyArmani">VoidbyArmani</option> - <option value="BlanchedAlmond">BlanchedAlmond</option> - <option value="BleudeFrance">BleudeFrance</option> - <option value="BlizzardBlue">BlizzardBlue</option> - <option value="Blond">Blond</option> - <option value="Blue">Blue</option> - <option value="BlueBell">BlueBell</option> - <option value="BlueGray">BlueGray</option> - <option value="Bluegreen">Bluegreen</option> - <option value="Blueviolet">Blueviolet</option> - <option value="Blush">Blush</option> - <option value="Bole">Bole</option> - <option value="Bondiblue">Bondiblue</option> - <option value="Brandeisblue">Brandeisblue</option> - <option value="Brass">Brass</option> - <option value="Brickred">Brickred</option> - <option value="Brightcerulean">Brightcerulean</option> - <option value="Brightgreen">Brightgreen</option> - <option value="Brightlavender">Brightlavender</option> - <option value="Brightmaroon">Brightmaroon</option> - <option value="Brightpink">Brightpink</option> - <option value="Brightturquoise">Brightturquoise</option> - <option value="Brightube">Brightube</option> - <option value="Brilliantlavender">Brilliantlavender</option> - <option value="Brilliantrose">Brilliantrose</option> - <option value="Brinkpink">Brinkpink</option> - <option value="Britishracinggreen">Britishracinggreen</option> - <option value="Bronze">Bronze</option> - <option value="Brown">Brown</option> - <option value="Bubblegum">Bubblegum</option> - <option value="Bubbles">Bubbles</option> - <option value="Buff">Buff</option> - <option value="Bulgarianrose">Bulgarianrose</option> - <option value="Burgundy">Burgundy</option> - <option value="Beaublue">Beaublue</option> - <option value="Burlywood">Burlywood</option> - <option value="Burntorange">Burntorange</option> - <option value="Burntsienna">Burntsienna</option> - <option value="Burntumber">Burntumber</option> - <option value="Bittersweet">Bittersweet</option> - <option value="Byzantine">Byzantine</option> - <option value="Byzantium">Byzantium</option> - <option value="Cadet">Cadet</option> - <option value="Cadetblue">Cadetblue</option> - <option value="Cadetgray">Cadetgray</option> - <option value="CadmiumGreen">CadmiumGreen</option> - <option value="CadmiumOrange">CadmiumOrange</option> - <option value="CadmiumRed">CadmiumRed</option> - <option value="CadmiumYellow">CadmiumYellow</option> - <option value="CalPolyPomonagreen">CalPolyPomonagreen</option> - <option value="CambridgeBlue">CambridgeBlue</option> - <option value="Camel">Camel</option> - <option value="Camouflagegreen">Camouflagegreen</option> - <option value="Canaryyellow">Canaryyellow</option> - <option value="Candyapplered">Candyapplered</option> - <option value="Candypink">Candypink</option> - <option value="Capri">Capri</option> - <option value="Caputmortuum">Caputmortuum</option> - <option value="Cardinal">Cardinal</option> - <option value="Caribbeangreen">Caribbeangreen</option> - <option value="Carmine">Carmine</option> - <option value="Carminepink">Carminepink</option> - <option value="Carminered">Carminered</option> - <option value="Carnationpink">Carnationpink</option> - <option value="Carnelian">Carnelian</option> - <option value="Carolinablue">Carolinablue</option> - <option value="Carrotorange">Carrotorange</option> - <option value="Ceil">Ceil</option> - <option value="Celadon">Celadon</option> - <option value="Celestialblue">Celestialblue</option> - <option value="Cerise">Cerise</option> - <option value="Cerisepink">Cerisepink</option> - <option value="Cerulean">Cerulean</option> - <option value="Ceruleanblue">Ceruleanblue</option> - <option value="CGBlue">CGBlue</option> - <option value="CGRed">CGRed</option> - <option value="Chamoisee">Chamoisee</option> - <option value="Champagne">Champagne</option> - <option value="Charcoal">Charcoal</option> - <option value="Chartreuse">Chartreuse</option> - <option value="Cherryblossompink">Cherryblossompink</option> - <option value="Chestnut">Chestnut</option> - <option value="Chocolate">Chocolate</option> - <option value="Chromeyellow">Chromeyellow</option> - <option value="Cinereous">Cinereous</option> - <option value="Cinnabar">Cinnabar</option> - <option value="Cinnamon">Cinnamon</option> - <option value="Citrine">Citrine</option> - <option value="Classicrose">Classicrose</option> - <option value="Cobalt">Cobalt</option> - <option value="Coffee">Coffee</option> - <option value="Columbiablue">Columbiablue</option> - <option value="Coolblack">Coolblack</option> - <option value="Coolgray">Coolgray</option> - <option value="Copper">Copper</option> - <option value="Copperrose">Copperrose</option> - <option value="Coquelicot">Coquelicot</option> - <option value="Coral">Coral</option> - <option value="Coralpink">Coralpink</option> - <option value="Coralred">Coralred</option> - <option value="Cordovan">Cordovan</option> - <option value="Corn">Corn</option> - <option value="Cornflowerblue">Cornflowerblue</option> - <option value="Cornsilk">Cornsilk</option> - <option value="Cosmiclatte">Cosmiclatte</option> - <option value="Cottoncandy">Cottoncandy</option> - <option value="Cream">Cream</option> - <option value="Crimson">Crimson</option> - <option value="Crimsonglory">Crimsonglory</option> - <option value="Cyan">Cyan</option> - <option value="Daffodil">Daffodil</option> - <option value="Dandelion">Dandelion</option> - <option value="Darkblue">Darkblue</option> - <option value="Darkbrown">Darkbrown</option> - <option value="Darkbyzantium">Darkbyzantium</option> - <option value="Darkcandyapplered">Darkcandyapplered</option> - <option value="Darkcerulean">Darkcerulean</option> - <option value="Darkchampagne">Darkchampagne</option> - <option value="Darkchestnut">Darkchestnut</option> - <option value="Darkcoral">Darkcoral</option> - <option value="Darkcyan">Darkcyan</option> - <option value="Darkelectricblue">Darkelectricblue</option> - <option value="Darkgoldenrod">Darkgoldenrod</option> - <option value="Darkgray">Darkgray</option> - <option value="Darkgreen">Darkgreen</option> - <option value="Darkjunglegreen">Darkjunglegreen</option> - <option value="Darkkhaki">Darkkhaki</option> - <option value="Darklava">Darklava</option> - <option value="Darklavender">Darklavender</option> - <option value="Darkmagenta">Darkmagenta</option> - <option value="Darkmidnightblue">Darkmidnightblue</option> - <option value="Darkolivegreen">Darkolivegreen</option> - <option value="Darkorange">Darkorange</option> - <option value="Darkorchid">Darkorchid</option> - <option value="Darkpastelblue">Darkpastelblue</option> - <option value="Darkpastelgreen">Darkpastelgreen</option> - <option value="Darkpastelpurple">Darkpastelpurple</option> - <option value="Darkpastelred">Darkpastelred</option> - <option value="Darkpink">Darkpink</option> - <option value="Darkpowderblue">Darkpowderblue</option> - <option value="Darkraspberry">Darkraspberry</option> - <option value="Darkred">Darkred</option> - <option value="Darksalmon">Darksalmont</option> - <option value="Darkscarlet">Darkscarlet</option> - <option value="Darkseagreen">Darkseagreen</option> - <option value="Darksienna">Darksienna</option> - <option value="Darkslateblue">Darkslateblue</option> - <option value="Darkslategray">Darkslategray</option> - <option value="Darkspringgreen">Darkspringgreen</option> - <option value="Darktan">Darktan</option> - <option value="Darktangerine">Darktangerine</option> - <option value="Darkterracotta">Darkterracotta</option> - <option value="Darkturquoise">Darkturquoise</option> - <option value="Darkviolet">Darkviolet</option> - <option value="Dartmouthgreen">Dartmouthgreen</option> - <option value="Davysgray">Davysgray</option> - <option value="Debianred">Debianred</option> - <option value="Deepcarmine">Deepcarmine</option> - <option value="Deepcarminepink">Deepcarminepink</option> - <option value="Deepcarrotorange">Deepcarrotorange</option> - <option value="Deepcerise">Deepcerise</option> - <option value="Deepchampagne">Deepchampagne</option> - <option value="Deepchestnut">Deepchestnut</option> - <option value="Deepfuchsia">Deepfuchsia</option> - <option value="Deepjunglegreen">Deepjunglegreen</option> - <option value="Deeplilac">Deeplilac</option> - <option value="Deepmagenta">Deepmagenta</option> - <option value="Deeppeach">Deeppeach</option> - <option value="Deeppink">Deeppink</option> - <option value="Deepsaffron">Deepsaffron</option> - <option value="Denim">Denim</option> - <option value="Desertsand">Desertsand</option> - <option value="Dimgray">Dimgray</option> - <option value="Dodgerblue">Dodgerblue</option> - <option value="Dogwoodrose">Dogwoodrose</option> - <option value="Dollarbill">Dollarbill</option> - <option value="Drab">Drab</option> - <option value="Dukeblue">Dukeblue</option> - <option value="Earthyellow">Earthyellow</option> - <option value="Eggplant">Eggplant</option> - <option value="Egyptianblue">Egyptianblue</option> - <option value="Electricblue">Electricblue</option> - <option value="Electriccrimson">Electriccrimson</option> - <option value="Electricgreen">Electricgreen</option> - <option value="Electricindigo">Electricindigo</option> - <option value="Electriclime">Electriclime</option> - <option value="Electricpurple">Electricpurple</option> - <option value="Electricultramarine">Electricultramarine</option> - <option value="Electricviolet">Electricviolet</option> - <option value="Electricyellow">Electricyellow</option> - <option value="Emerald">Emerald</option> - <option value="Etonblue">Etonblue</option> - <option value="Falured">Falured</option> - <option value="Fandango">Fandango</option> - <option value="Fashionfuchsia">Fashionfuchsia</option> - <option value="Fawn">Fawn</option> - <option value="Feldgrau">Feldgrau</option> - <option value="Ferngreen">Ferngreen</option> - <option value="FerrariRed">FerrariRed</option> - <option value="Fielddrab">Fielddrab</option> - <option value="Firebrick">Firebrick</option> - <option value="Fireenginered">Fireenginered</option> - <option value="Flame">Flame</option> - <option value="Flamingopink">Flamingopink</option> - <option value="Flavescent">Flavescent</option> - <option value="Flax">Flax</option> - <option value="Floralwhite">Floralwhite</option> - <option value="Folly">Folly</option> - <option value="Forestgreen">Forestgreen</option> - <option value="Frenchbeige">Frenchbeige</option> - <option value="Frenchblue">Frenchblue</option> - <option value="Frenchlilac">Frenchlilac</option> - <option value="Frenchrose">Frenchrose</option> - <option value="Fuchsia">Fuchsia</option> - <option value="Fuchsiapink">Fuchsiapink</option> - <option value="Fulvous">Fulvous</option> - <option value="FuzzyWuzzy">FuzzyWuzzy</option> - <option value="Gainsboro">Gainsboro</option> - <option value="Gamboge">Gamboge</option> - <option value="Ghostwhite">Ghostwhite</option> - <option value="Ginger">Ginger</option> - <option value="Glaucous">Glaucous</option> - <option value="Gold">Gold</option> - <option value="Goldenbrown">Goldenbrown</option> - <option value="Goldenpoppy">Goldenpoppy</option> - <option value="Goldenrod">Goldenrod</option> - <option value="Goldenyellow">Goldenyellow</option> - <option value="GrannySmithApple">GrannySmithApple</option> - <option value="Gray">Gray</option> - <option value="Grayasparagus">Grayasparagus</option> - <option value="Green">Green</option> - <option value="Greenyellow">Greenyellow</option> - <option value="Grullo">Grullo</option> - <option value="Guppiegreen">Guppiegreen</option> - <option value="Halayaube">Halayaube</option> - <option value="Hanblue">Hanblue</option> - <option value="Hanpurple">Hanpurple</option> - <option value="Harlequin">Harlequin</option> - <option value="Harvardcrimson">Harvardcrimson</option> - <option value="HarvestGold">HarvestGold</option> - <option value="Heliotrope">Heliotrope</option> - <option value="Honeydew">Honeydew</option> - <option value="Hookersgreen">Hookersgreen</option> - <option value="Hotmagenta">Hotmagenta</option> - <option value="Hotpink">Hotpink</option> - <option value="Huntergreen">Huntergreen</option> - <option value="Iceberg">Iceberg</option> - <option value="Icterine">Icterine</option> - <option value="Inchworm">Inchworm</option> - <option value="Indiagreen">Indiagreen</option> - <option value="Indianyellow">Indianyellow</option> - <option value="Indigo">Indigo</option> - <option value="InternationalKleinBlue">InternationalKleinBlue</option> - <option value="Internationalorange">Internationalorange</option> - <option value="Iris">Iris</option> - <option value="Isabelline">Isabelline</option> - <option value="Islamicgreen">Islamicgreen</option> - <option value="Ivory">Ivory</option> - <option value="Jade">Jade</option> - <option value="Jasmine">Jasmine</option> - <option value="Jasper">Jasper</option> - <option value="Jazzberryjam">Jazzberryjam</option> - <option value="Jonquil">Jonquil</option> - <option value="Junebud">Junebud</option> - <option value="Junglegreen">Junglegreen</option> - <option value="Kellygreen">Kellygreen</option> - <option value="Khaki">Khaki</option> - <option value="KUCrimson">KUCrimson</option> - <option value="Languidlavender">Languidlavender</option> - <option value="Lapislazuli">Lapislazuli</option> - <option value="LaSalleGreen">LaSalleGreen</option> - <option value="LaserLemo">LaserLemo</option> - <option value="Lava">Lava</option> - <option value="Lavender">Lavender</option> - <option value="Lavenderblue">Lavenderblue</option> - <option value="Lavenderblush">Lavenderblush</option> - <option value="Lavendergray">Lavendergray</option> - <option value="Lavendermagenta">Lavendermagenta</option> - <option value="Lavendermist">Lavendermist</option> - <option value="Lavenderpink">Lavenderpink</option> - <option value="Lavenderpurple">Lavenderpurple</option> - <option value="Lavenderrose">Lavenderrose</option> - <option value="Lawngreen">Lawngren</option> - <option value="Lemon">Lemon</option> - <option value="Lemonchiffon">Lemonchiffon</option> - <option value="Lightapricot">Lightapricot</option> - <option value="Lightblue">Lightblue</option> - <option value="Lightbrown">Lightbrown</option> - <option value="Lightcarminepink">Lightcarminepink</option> - <option value="Lightcoral">Lightcoral</option> - <option value="Lightcornflowerblue">Lightcornflowerblue</option> - <option value="LightCrimson">LightCrimson</option> - <option value="Lightcyan">Lightcyan</option> - <option value="Lightfuchsiapink">Lightfuchsiapink</option> - <option value="Lightgoldenrodyellow">Lightgoldenrodyellow</option> - <option value="Lightgray">Lightgray</option> - <option value="Lightgreen">Lightgreen</option> - <option value="Lightkhaki">Lightkhaki</option> - <option value="Lightmauve">Lightmauve</option> - <option value="Lightpastelpurple">Lightpastelpurple</option> - <option value="Lightpink">Lightpink</option> - <option value="Lightsalmon">Lightsalmon</option> - <option value="Lightsalmonpink">Lightsalmonpink</option> - <option value="Lightseagreen">Lightseagreen</option> - <option value="Lightskyblue">Lightskyblue</option> - <option value="Lightslategray">Lightslategray</option> - <option value="Lighttaupe">Lighttaupe</option> - <option value="LightThulianpink">LightThulianpink</option> - <option value="Lightyellow">Lightyellow</option> - <option value="Lilac">Lilac</option> - <option value="Lime">Lime</option> - <option value="Limegreen">Limegreen</option> - <option value="Lincolngreen">Lincolngreen</option> - <option value="Linen">Linen</option> - <option value="Liver">Liver</option> - <option value="Lust">Lust</option> - <option value="Magenta">Magenta</option> - <option value="Magicmint">Magicmint</option> - <option value="Magnolia">Magnolia</option> - <option value="Mahogany">Mahogany</option> - <option value="MajorelleBlue">MajorelleBlue</option> - <option value="Malachite">Malachite</option> - <option value="Manatee">Manatee</option> - <option value="MangoTango">MangoTango</option> - <option value="Maroon">Maroon</option> - <option value="Mauve">Mauve</option> - <option value="Mauvelous">Mauvelous</option> - <option value="Mauvetaupe">Mauvetaupe</option> - <option value="Mayablue">Mayablue</option> - <option value="Meatbrown">Meatbrown</option> - <option value="Mediumaquamarine">Mediumaquamarine</option> - <option value="Mediumblue">Mediumblue</option> - <option value="Mediumcandyapplered">Mediumcandyapplered</option> - <option value="Mediumcarmine">Mediumcarmine</option> - <option value="Mediumchampagne">Mediumchampagne</option> - <option value="Mediumelectricblue">Mediumelectricblue</option> - <option value="Mediumjunglegreen">Mediumjunglegreen</option> - <option value="Mediumlavendermagenta">Mediumlavendermagenta</option> - <option value="Mediumorchid">Mediumorchid</option> - <option value="MediumPersianblue">MediumPersianblue</option> - <option value="Mediumpurple">Mediumpurple</option> - <option value="Mediumredviolet">Mediumredviolet</option> - <option value="Mediumseagreen">Mediumseagreen</option> - <option value="Atomictangerine">Atomictangerine</option> - <option value="Mediumslateblue">Mediumslateblue</option> - <option value="Mediumspringbud">Mediumspringbud</option> - <option value="Mediumspringgreen">Mediumspringgreen</option> - <option value="Mediumtaupe">Mediumtaupe</option> - <option value="Mediumtealblue">Mediumtealblue</option> - <option value="Mediumturquoise">Mediumturquoise</option> - <option value="Mediumvioletred">Mediumvioletred</option> - <option value="Melon">Melon</option> - <option value="Midnightblue">Midnightblue</option> - <option value="Midnightgreen">Midnightgreen</option> - <option value="Mikadoyellow">Mikadoyellow</option> - <option value="Mint">Mint</option> - <option value="Mintcream">Mintcream</option> - <option value="Mintgreen">Mintgreen</option> - <option value="Mistyrose">Mistyrose</option> - <option value="Moonstoneblue">Moonstoneblue</option> - <option value="Mordantred19">Mordantred19e</option> - <option value="Mossgreen">Mossgreen</option> - <option value="MountainMeadow">MountainMeadow</option> - <option value="Mountbattenpink">Mountbattenpink</option> - <option value="MSUGreen">MSUGreenl</option> - <option value="Midnight">Midnight</option> - <option value="Mulberry">Mulberry</option> - <option value="Mustard">Mustard</option> - <option value="Myrtle">Myrtle</option> - <option value="Nadeshikopink">Nadeshikopink</option> - <option value="Napiergreen">Napiergreen</option> - <option value="Navajowhite">Navajowhite</option> - <option value="Neonfuchsia">Neonfuchsia</option> - <option value="Neongreen">Neongreen</option> - <option value="Nonphotoblue">Nonphotoblue</option> - <option value="OceanBoatBlu">OceanBoatBlu</option> - <option value="Ochre">Ochre</option> - <option value="Oldgold">Oldgold</option> - <option value="Oldlace">Oldlace</option> - <option value="Oldlavender">Oldlavender</option> - <option value="Oldmauve">Oldmauve</option> - <option value="Oldrose">Oldrose</option> - <option value="Olive">Olive</option> - <option value="OliveDrab">OliveDrab</option> - <option value="OliveDrab7">OliveDrab7</option> - <option value="Olivine">Olivine</option> - <option value="Operamauve">Operamauve</option> - <option value="Orange">Orange</option> - <option value="Orangepeel">Orangepeel</option> - <option value="Orangered">Orangered</option> - <option value="Orchid">Orchid</option> - <option value="OUCrimsonRed">OUCrimsonRed</option> - <option value="OuterSpace">OuterSpace</option> - <option value="OutrageousOrange">OutrageousOrange</option> - <option value="OxfordBlue">OxfordBlue</option> - <option value="Pakistangreen">Pakistangreen</option> - <option value="Palatinateblue">Palatinateblue</option> - <option value="Palatinatepurple">Palatinatepurple</option> - <option value="Paleblue">Paleblue</option> - <option value="Palebrown">Palebrown</option> - <option value="Palecerulean">Palecerulean</option> - <option value="Palechestnut">Palechestnut</option> - <option value="Palecopper">Palecopper</option> - <option value="Palecornflowerblue">Palecornflowerblue</option> - <option value="Palegold">Palegolde</option> - <option value="Palegreen">Palegreen</option> - <option value="Palemagenta">Palemagenta</option> - <option value="Palepink">Palepink</option> - <option value="Paleredviolet">Paleredviolet</option> - <option value="Palerobineggblue">Palerobineggblue</option> - <option value="Palesilver">Palesilver</option> - <option value="Palespringbud">Palespringbud</option> - <option value="Paletaupe">Paletaupe</option> - <option value="Pansypurple">Pansypurple</option> - <option value="Papayawhip">Papayawhip</option> - <option value="Pastelblue">Pastelblue</option> - <option value="Pastelbrown">Pastelbrown</option> - <option value="Pastelgray">Pastelgray</option> - <option value="Pastelgreen">Pastelgreen</option> - <option value="Pastelmagenta">Pastelmagenta</option> - <option value="Pastelorange">Pastelorange</option> - <option value="Pastelpink">Pastelpink</option> - <option value="Pastelpurple">Pastelpurple</option> - <option value="Pastelred">Pastelred</option> - <option value="Pastelviolet">Pastelviolet</option> - <option value="Pastelyellow">Pastelyellow</option> - <option value="Paynesgray">Paynesgray</option> - <option value="Peach">Peach</option> - <option value="Peachorange">Peachorange</option> - <option value="Peachpuff">Peachpuff</option> - <option value="Peachyellow">Peachyellow</option> - <option value="Pear">Pear</option> - <option value="PearlAqua">PearlAqua</option> - <option value="Peridot">Peridot</option> - <option value="Persianblue">Persianblue</option> - <option value="Persiangreen">Persiangreen</option> - <option value="Persianindigo">Persianindigo</option> - <option value="Persianorange">Persianorange</option> - <option value="Persianpink">Persianpink</option> - <option value="Persianplum">Persianplum</option> - <option value="Persianred">Persianred</option> - <option value="Persianrose">Persianrose</option> - <option value="Persimmon">Persimmon</option> - <option value="Phlox">Phlox</option> - <option value="Phthaloblue">Phthaloblue</option> - <option value="Phthalogreen">Phthalogreen</option> - <option value="Piggypink">Piggypink</option> - <option value="Pinegreen">Pinegreen</option> - <option value="Pink">Pink</option> - <option value="Pinkpearl">Pinkpearl</option> - <option value="PinkSherbet">PinkSherbet</option> - <option value="Pistachio">Pistachio</option> - <option value="Platinum">Platinum</option> - <option value="Plum">Plum</option> - <option value="PortlandOrange">PortlandOrange</option> - <option value="Powderblue">Powderblue</option> - <option value="Princetonorange">Princetonorange</option> - <option value="Prussianblue">Prussianblue</option> - <option value="Puce">Puce</option> - <option value="Pumpkin">Pumpkin</option> - <option value="Purple">Purple</option> - <option value="PurpleHeart">PurpleHeart</option> - <option value="Purplemountainmajesty">Purplemountainmajesty</option> - <option value="Purplepizzazz">Purplepizzazz</option> - <option value="Purpletaupe">Purpletaupe</option> - <option value="Quartz">Quartz</option> - <option value="RadicalRed">RadicalRed</option> - <option value="Raspberry">Raspberry</option> - <option value="Raspberrypink">Raspberrypink</option> - <option value="Raspberryrose">Raspberryrose</option> - <option value="Rawumber">Rawumber</option> - <option value="Razzledazzlerose">Razzledazzlerose</option> - <option value="Razzmatazz">Razzmatazz</option> - <option value="Red">Red</option> - <option value="Redwood">Redwood</option> - <option value="Regalia">Regalia</option> - <option value="Richblack">Richblack</option> - <option value="Richbrilliantlavender">Richbrilliantlavender</option> - <option value="Richcarmine">Richcarmine</option> - <option value="Richelectricblue">Richelectricblue</option> - <option value="Richlavender">Richlavender</option> - <option value="Richlilac">Richlilac</option> - <option value="Richmaroon">Richmaroon</option> - <option value="Riflegreen">Riflegreen</option> - <option value="Robineggblue">Robineggblue</option> - <option value="Rosebonbon">Rosebonbon</option> - <option value="Roseebony">Roseebony</option> - <option value="Rosegold">Rosegold</option> - <option value="Rosepink">Rosepink</option> - <option value="Rosequartz">Rosequartz</option> - <option value="Rosetaupe">Rosetaupe</option> - <option value="Rosewood">Rosewood</option> - <option value="Rossocorsa">Rossocorsa</option> - <option value="Rosybrown">Rosybrown</option> - <option value="Royalazure">Royalazure</option> - <option value="Royalblue">Royalblue</option> - <option value="Royalfuchsia">Royalfuchsia</option> - <option value="Royalpurple">Royalpurple</option> - <option value="Ruby">Ruby</option> - <option value="Ruddy">Ruddy</option> - <option value="Ruddybrown">Ruddybrown</option> - <option value="Ruddypink">Ruddypink</option> - <option value="Rufous">Rufouse</option> - <option value="Russet">Russet</option> - <option value="Rust">Rust</option> - <option value="SacramentoStategreen">SacramentoStategreen</option> - <option value="Saddlebrown">Saddlebrown</option> - <option value="Safetyorange">Safetyorange</option> - <option value="Saffron">Saffron</option> - <option value="Salmon">Salmon</option> - <option value="Salmonpink">Salmonpink</option> - <option value="Sandstorm">Sandstorm</option> - <option value="Sandybrown">Sandybrown</option> - <option value="Sangria">Sangria</option> - <option value="Sapgreen">Sapgreen</option> - <option value="Sapphire">Sapphire</option> - <option value="Satinsheengold">Satinsheengold</option> - <option value="Scarlet">Scarlet</option> - <option value="Schoolbusyellow">Schoolbusyellow</option> - <option value="ScreaminGreen">ScreaminGreen</option> - <option value="Seagreen">Seagreen</option> - <option value="Sealbrown">Sealbrown</option> - <option value="Seashell">Seashell</option> - <option value="Selectiveyellow">Selectiveyellow</option> - <option value="Sepia">Sepia</option> - <option value="Shadow">Shadow</option> - <option value="Shamrockgreen">Shamrockgreen</option> - <option value="Shockingpink">Shockingpink</option> - <option value="Sienna">Sienna</option> - <option value="Silver">Silver</option> - <option value="Sinopia">Sinopia</option> - <option value="Skobeloff">Skobeloff</option> - <option value="Skyblue">Skyblue</option> - <option value="Skymagenta">Skymagenta</option> - <option value="Slateblue">Slateblue</option> - <option value="Slategray">Slategrayh</option> - <option value="Smokeytopaz">Smokeytopaz</option> - <option value="Smokyblack">Smokyblack</option> - <option value="Snow">Snow</option> - <option value="SpiroDiscoBall">SpiroDiscoBalld</option> - <option value="Splashedwhite">Splashedwhite</option> - <option value="Springbud">Springbud</option> - <option value="Steelblue">Steelblue</option> - <option value="St.Patricksblue">St.Patricksblue</option> - <option value="Straw">Straw</option> - <option value="Tan">Tan</option> - <option value="Tangelo">Tangelo</option> - <option value="Tangerine">Tangerine</option> - <option value="Tangerineyellow">Tangerineyellow</option> - <option value="Taupegray">Taupegray</option> - <option value="Teagreen">Teagreen</option> - <option value="Teal">Teal</option> - <option value="Tealblue">Tealblue</option> - <option value="Tealgreen">Tealgreen</option> - <option value="Tenné">Tenné</option> - <option value="Terracotta">Terracotta</option> - <option value="Thistle">Thistle</option> - <option value="Thulianpink">Thulianpink</option> - <option value="TickleMePink">TickleMePink</option> - <option value="TiffanyBlue">TiffanyBlue</option> - <option value="Tigerseye">Tigerseye</option> - <option value="Timberwolf">Timberwolf</option> - <option value="Titaniumyellow">Titaniumyellow</option> - <option value="Tomato">Tomato</option> - <option value="Toolbox">Toolbox</option> - <option value="Topaz">Topaz</option> - <option value="Tractorred">Tractorred</option> - <option value="Tropicalrainforest">Tropicalrainforest</option> - <option value="TrueBlue">TrueBlue</option> - <option value="TuftsBlue">TuftsBlue</option> - <option value="Tumbleweed">Tumbleweed</option> - <option value="Turkishrose">Turkishrose</option> - <option value="Turquoise">Turquoise</option> - <option value="Turquoiseblue">Turquoiseblue</option> - <option value="Turquoisegreen">Turquoisegreen</option> - <option value="Tuscanred">Tuscanred</option> - <option value="Twilightlavender">Twilightlavender</option> - <option value="Tyrianpurple">Tyrianpurple</option> - <option value="UAblue">UAblue</option> - <option value="UAred">UAred</option> - <option value="Ube">Ube</option> - <option value="UCLABlue">UCLABlue</option> - <option value="UCLAGold">UCLAGold</option> - <option value="UFOGreen">UFOGreen</option> - <option value="Ultramarine">Ultramarine</option> - <option value="Ultramarineblue">Ultramarineblue</option> - <option value="Ultrapink">Ultrapink</option> - <option value="UnitedNationsblue">UnitedNationsblue</option> - <option value="UniversityofCaliforniaGold">UniversityofCaliforniaGold</option> - <option value="UnmellowYellow">UnmellowYellow</option> - <option value="UPMaroon">UPMaroon</option> - <option value="Upsdellred">Upsdellred</option> - <option value="Urobilin">Urobilin</option> - <option value="UtahCrimson">UtahCrimson</option> - <option value="Vegasgold">Vegasgold</option> - <option value="Venetianred">Venetianred</option> - <option value="Verdigris">Verdigris</option> - <option value="Veronica">Veronica</option> - <option value="Violet">Violet</option> - <option value="Viridian">Viridian</option> - <option value="Vividauburn">Vividauburn</option> - <option value="Vividburgundy">Vividburgundy</option> - <option value="Vividceris">Vividceris</option> - <option value="Vividtangerine">Vividtangerine</option> - <option value="Vividviolet">Vividviolet</option> - <option value="Warmblack">Warmblack</option> - <option value="Wenge">Wenge</option> - <option value="Wheat">Wheat</option> - <option value="White">White</option> - <option value="Whitesmoke">Whitesmoke</option> - <option value="Wildblueyonder">Wildblueyonder</option> - <option value="WildStrawberry">WildStrawberry</option> - <option value="WildWatermelon">WildWatermelon</option> - <option value="Wine">Wine</option> - <option value="Wisteria">Wisteria</option> - <option value="Xanadu">Xanadu</option> - <option value="YaleBlue">YaleBlue</option> - <option value="Yellow">Yellow</option> - <option value="Yellowgreen">Yellowgreen</option> - <option value="YellowOrange">YellowOrange</option> - <option value="Zaffre">Zaffre</option> - <option value="Zinnwalditebrown">Zinnwalditebrown</option> - </param> - <param name="outline_color" type="select" label="Outline Color" > - <option value="black">Black</option> - <option value="white">White</option> - </param> - <param name="filt_color" type="select" label="Crapome Filter Color" > - <option value="AirForceblue">AirForceblue</option> - <option value="Aliceblue">Aliceblue</option> - <option value="Alizarincrimson">Alizarincrimson</option> - <option value="Almond">Almond</option> - <option value="Amaranth">Amaranth</option> - <option value="Amber">Amber</option> - <option value="Americanrose">Americanrose</option> - <option value="Amethyst">Amethyst</option> - <option value="AndroidGreen">AndroidGreen</option> - <option value="AirForceblue">Antiflashwhite</option> - <option value="Antiquefuchsia">Antiquefuchsia</option> - <option value="Antiquewhite">Antiquewhite</option> - <option value="Ao">Ao</option> - <option value="Applegreen">Applegreen</option> - <option value="Apricot">Apricot</option> - <option value="Aqua">Aqua</option> - <option value="Amber">Amber</option> - <option value="Aquamarine">Aquamarine</option> - <option value="Amethyst">Amethyst</option> - <option value="Armygreen">Armygreen</option> - <option value="Arsenic">Arsenic</option> - <option value="Arylideyellow">Arylideyellow</option> - <option value="Ashgray">Ashgray</option> - <option value="Asparagus">Asparagus</option> - <option value="Atomictangerine">Atomictangerine</option> - <option value="Auburn">Auburn</option> - <option value="Aureolin">Aureolin</option> - <option value="AuroMetalSaurus">AuroMetalSaurus</option> - <option value="Awesome">Awesome</option> - <option value="Azuremist">Azuremist</option> - <option value="Babyblue">Babyblue</option> - <option value="Babypink">Babypink</option> - <option value="BallBlue">BallBlue</option> - <option value="BananaMania">BananaMania</option> - <option value="Bananayellow">Bananayellow</option> - <option value="Battleshipgray">Battleshipgray</option> - <option value="Bazaar">Bazaar</option> - <option value="Beaublue">Beaublue</option> - <option value="Beaver">Beaver</option> - <option value="Beige">Beige</option> - <option value="Bisque">Bisque</option> - <option value="Bistre">Bistre</option> - <option value="Bittersweet">Bittersweet</option> - <option value="Obsidian">Obsidian</option> - <option value="Onyx">Onyx</option> - <option value="LostSoul">LostSoul</option> - <option value="Midnight">Midnight</option> - <option value="RollingBlackout">RollingBlackout</option> - <option value="SleepingPanther">SleepingPanther</option> - <option value="VoidbyArmani">VoidbyArmani</option> - <option value="BlanchedAlmond">BlanchedAlmond</option> - <option value="BleudeFrance">BleudeFrance</option> - <option value="BlizzardBlue">BlizzardBlue</option> - <option value="Blond">Blond</option> - <option value="Blue">Blue</option> - <option value="BlueBell">BlueBell</option> - <option value="BlueGray">BlueGray</option> - <option value="Bluegreen">Bluegreen</option> - <option value="Blueviolet">Blueviolet</option> - <option value="Blush">Blush</option> - <option value="Bole">Bole</option> - <option value="Bondiblue">Bondiblue</option> - <option value="Brandeisblue">Brandeisblue</option> - <option value="Brass">Brass</option> - <option value="Brickred">Brickred</option> - <option value="Brightcerulean">Brightcerulean</option> - <option value="Brightgreen">Brightgreen</option> - <option value="Brightlavender">Brightlavender</option> - <option value="Brightmaroon">Brightmaroon</option> - <option value="Brightpink">Brightpink</option> - <option value="Brightturquoise">Brightturquoise</option> - <option value="Brightube">Brightube</option> - <option value="Brilliantlavender">Brilliantlavender</option> - <option value="Brilliantrose">Brilliantrose</option> - <option value="Brinkpink">Brinkpink</option> - <option value="Britishracinggreen">Britishracinggreen</option> - <option value="Bronze">Bronze</option> - <option value="Brown">Brown</option> - <option value="Bubblegum">Bubblegum</option> - <option value="Bubbles">Bubbles</option> - <option value="Buff">Buff</option> - <option value="Bulgarianrose">Bulgarianrose</option> - <option value="Burgundy">Burgundy</option> - <option value="Beaublue">Beaublue</option> - <option value="Burlywood">Burlywood</option> - <option value="Burntorange">Burntorange</option> - <option value="Burntsienna">Burntsienna</option> - <option value="Burntumber">Burntumber</option> - <option value="Bittersweet">Bittersweet</option> - <option value="Byzantine">Byzantine</option> - <option value="Byzantium">Byzantium</option> - <option value="Cadet">Cadet</option> - <option value="Cadetblue">Cadetblue</option> - <option value="Cadetgray">Cadetgray</option> - <option value="CadmiumGreen">CadmiumGreen</option> - <option value="CadmiumOrange">CadmiumOrange</option> - <option value="CadmiumRed">CadmiumRed</option> - <option value="CadmiumYellow">CadmiumYellow</option> - <option value="CalPolyPomonagreen">CalPolyPomonagreen</option> - <option value="CambridgeBlue">CambridgeBlue</option> - <option value="Camel">Camel</option> - <option value="Camouflagegreen">Camouflagegreen</option> - <option value="Canaryyellow">Canaryyellow</option> - <option value="Candyapplered">Candyapplered</option> - <option value="Candypink">Candypink</option> - <option value="Capri">Capri</option> - <option value="Caputmortuum">Caputmortuum</option> - <option value="Cardinal">Cardinal</option> - <option value="Caribbeangreen">Caribbeangreen</option> - <option value="Carmine">Carmine</option> - <option value="Carminepink">Carminepink</option> - <option value="Carminered">Carminered</option> - <option value="Carnationpink">Carnationpink</option> - <option value="Carnelian">Carnelian</option> - <option value="Carolinablue">Carolinablue</option> - <option value="Carrotorange">Carrotorange</option> - <option value="Ceil">Ceil</option> - <option value="Celadon">Celadon</option> - <option value="Celestialblue">Celestialblue</option> - <option value="Cerise">Cerise</option> - <option value="Cerisepink">Cerisepink</option> - <option value="Cerulean">Cerulean</option> - <option value="Ceruleanblue">Ceruleanblue</option> - <option value="CGBlue">CGBlue</option> - <option value="CGRed">CGRed</option> - <option value="Chamoisee">Chamoisee</option> - <option value="Champagne">Champagne</option> - <option value="Charcoal">Charcoal</option> - <option value="Chartreuse">Chartreuse</option> - <option value="Cherryblossompink">Cherryblossompink</option> - <option value="Chestnut">Chestnut</option> - <option value="Chocolate">Chocolate</option> - <option value="Chromeyellow">Chromeyellow</option> - <option value="Cinereous">Cinereous</option> - <option value="Cinnabar">Cinnabar</option> - <option value="Cinnamon">Cinnamon</option> - <option value="Citrine">Citrine</option> - <option value="Classicrose">Classicrose</option> - <option value="Cobalt">Cobalt</option> - <option value="Coffee">Coffee</option> - <option value="Columbiablue">Columbiablue</option> - <option value="Coolblack">Coolblack</option> - <option value="Coolgray">Coolgray</option> - <option value="Copper">Copper</option> - <option value="Copperrose">Copperrose</option> - <option value="Coquelicot">Coquelicot</option> - <option value="Coral">Coral</option> - <option value="Coralpink">Coralpink</option> - <option value="Coralred">Coralred</option> - <option value="Cordovan">Cordovan</option> - <option value="Corn">Corn</option> - <option value="Cornflowerblue">Cornflowerblue</option> - <option value="Cornsilk">Cornsilk</option> - <option value="Cosmiclatte">Cosmiclatte</option> - <option value="Cottoncandy">Cottoncandy</option> - <option value="Cream">Cream</option> - <option value="Crimson">Crimson</option> - <option value="Crimsonglory">Crimsonglory</option> - <option value="Cyan">Cyan</option> - <option value="Daffodil">Daffodil</option> - <option value="Dandelion">Dandelion</option> - <option value="Darkblue">Darkblue</option> - <option value="Darkbrown">Darkbrown</option> - <option value="Darkbyzantium">Darkbyzantium</option> - <option value="Darkcandyapplered">Darkcandyapplered</option> - <option value="Darkcerulean">Darkcerulean</option> - <option value="Darkchampagne">Darkchampagne</option> - <option value="Darkchestnut">Darkchestnut</option> - <option value="Darkcoral">Darkcoral</option> - <option value="Darkcyan">Darkcyan</option> - <option value="Darkelectricblue">Darkelectricblue</option> - <option value="Darkgoldenrod">Darkgoldenrod</option> - <option value="Darkgray">Darkgray</option> - <option value="Darkgreen">Darkgreen</option> - <option value="Darkjunglegreen">Darkjunglegreen</option> - <option value="Darkkhaki">Darkkhaki</option> - <option value="Darklava">Darklava</option> - <option value="Darklavender">Darklavender</option> - <option value="Darkmagenta">Darkmagenta</option> - <option value="Darkmidnightblue">Darkmidnightblue</option> - <option value="Darkolivegreen">Darkolivegreen</option> - <option value="Darkorange">Darkorange</option> - <option value="Darkorchid">Darkorchid</option> - <option value="Darkpastelblue">Darkpastelblue</option> - <option value="Darkpastelgreen">Darkpastelgreen</option> - <option value="Darkpastelpurple">Darkpastelpurple</option> - <option value="Darkpastelred">Darkpastelred</option> - <option value="Darkpink">Darkpink</option> - <option value="Darkpowderblue">Darkpowderblue</option> - <option value="Darkraspberry">Darkraspberry</option> - <option value="Darkred">Darkred</option> - <option value="Darksalmon">Darksalmont</option> - <option value="Darkscarlet">Darkscarlet</option> - <option value="Darkseagreen">Darkseagreen</option> - <option value="Darksienna">Darksienna</option> - <option value="Darkslateblue">Darkslateblue</option> - <option value="Darkslategray">Darkslategray</option> - <option value="Darkspringgreen">Darkspringgreen</option> - <option value="Darktan">Darktan</option> - <option value="Darktangerine">Darktangerine</option> - <option value="Darkterracotta">Darkterracotta</option> - <option value="Darkturquoise">Darkturquoise</option> - <option value="Darkviolet">Darkviolet</option> - <option value="Dartmouthgreen">Dartmouthgreen</option> - <option value="Davysgray">Davysgray</option> - <option value="Debianred">Debianred</option> - <option value="Deepcarmine">Deepcarmine</option> - <option value="Deepcarminepink">Deepcarminepink</option> - <option value="Deepcarrotorange">Deepcarrotorange</option> - <option value="Deepcerise">Deepcerise</option> - <option value="Deepchampagne">Deepchampagne</option> - <option value="Deepchestnut">Deepchestnut</option> - <option value="Deepfuchsia">Deepfuchsia</option> - <option value="Deepjunglegreen">Deepjunglegreen</option> - <option value="Deeplilac">Deeplilac</option> - <option value="Deepmagenta">Deepmagenta</option> - <option value="Deeppeach">Deeppeach</option> - <option value="Deeppink">Deeppink</option> - <option value="Deepsaffron">Deepsaffron</option> - <option value="Denim">Denim</option> - <option value="Desertsand">Desertsand</option> - <option value="Dimgray">Dimgray</option> - <option value="Dodgerblue">Dodgerblue</option> - <option value="Dogwoodrose">Dogwoodrose</option> - <option value="Dollarbill">Dollarbill</option> - <option value="Drab">Drab</option> - <option value="Dukeblue">Dukeblue</option> - <option value="Earthyellow">Earthyellow</option> - <option value="Eggplant">Eggplant</option> - <option value="Egyptianblue">Egyptianblue</option> - <option value="Electricblue">Electricblue</option> - <option value="Electriccrimson">Electriccrimson</option> - <option value="Electricgreen">Electricgreen</option> - <option value="Electricindigo">Electricindigo</option> - <option value="Electriclime">Electriclime</option> - <option value="Electricpurple">Electricpurple</option> - <option value="Electricultramarine">Electricultramarine</option> - <option value="Electricviolet">Electricviolet</option> - <option value="Electricyellow">Electricyellow</option> - <option value="Emerald">Emerald</option> - <option value="Etonblue">Etonblue</option> - <option value="Falured">Falured</option> - <option value="Fandango">Fandango</option> - <option value="Fashionfuchsia">Fashionfuchsia</option> - <option value="Fawn">Fawn</option> - <option value="Feldgrau">Feldgrau</option> - <option value="Ferngreen">Ferngreen</option> - <option value="FerrariRed">FerrariRed</option> - <option value="Fielddrab">Fielddrab</option> - <option value="Firebrick">Firebrick</option> - <option value="Fireenginered">Fireenginered</option> - <option value="Flame">Flame</option> - <option value="Flamingopink">Flamingopink</option> - <option value="Flavescent">Flavescent</option> - <option value="Flax">Flax</option> - <option value="Floralwhite">Floralwhite</option> - <option value="Folly">Folly</option> - <option value="Forestgreen">Forestgreen</option> - <option value="Frenchbeige">Frenchbeige</option> - <option value="Frenchblue">Frenchblue</option> - <option value="Frenchlilac">Frenchlilac</option> - <option value="Frenchrose">Frenchrose</option> - <option value="Fuchsia">Fuchsia</option> - <option value="Fuchsiapink">Fuchsiapink</option> - <option value="Fulvous">Fulvous</option> - <option value="FuzzyWuzzy">FuzzyWuzzy</option> - <option value="Gainsboro">Gainsboro</option> - <option value="Gamboge">Gamboge</option> - <option value="Ghostwhite">Ghostwhite</option> - <option value="Ginger">Ginger</option> - <option value="Glaucous">Glaucous</option> - <option value="Gold">Gold</option> - <option value="Goldenbrown">Goldenbrown</option> - <option value="Goldenpoppy">Goldenpoppy</option> - <option value="Goldenrod">Goldenrod</option> - <option value="Goldenyellow">Goldenyellow</option> - <option value="GrannySmithApple">GrannySmithApple</option> - <option value="Gray">Gray</option> - <option value="Grayasparagus">Grayasparagus</option> - <option value="Green">Green</option> - <option value="Greenyellow">Greenyellow</option> - <option value="Grullo">Grullo</option> - <option value="Guppiegreen">Guppiegreen</option> - <option value="Halayaube">Halayaube</option> - <option value="Hanblue">Hanblue</option> - <option value="Hanpurple">Hanpurple</option> - <option value="Harlequin">Harlequin</option> - <option value="Harvardcrimson">Harvardcrimson</option> - <option value="HarvestGold">HarvestGold</option> - <option value="Heliotrope">Heliotrope</option> - <option value="Honeydew">Honeydew</option> - <option value="Hookersgreen">Hookersgreen</option> - <option value="Hotmagenta">Hotmagenta</option> - <option value="Hotpink">Hotpink</option> - <option value="Huntergreen">Huntergreen</option> - <option value="Iceberg">Iceberg</option> - <option value="Icterine">Icterine</option> - <option value="Inchworm">Inchworm</option> - <option value="Indiagreen">Indiagreen</option> - <option value="Indianyellow">Indianyellow</option> - <option value="Indigo">Indigo</option> - <option value="InternationalKleinBlue">InternationalKleinBlue</option> - <option value="Internationalorange">Internationalorange</option> - <option value="Iris">Iris</option> - <option value="Isabelline">Isabelline</option> - <option value="Islamicgreen">Islamicgreen</option> - <option value="Ivory">Ivory</option> - <option value="Jade">Jade</option> - <option value="Jasmine">Jasmine</option> - <option value="Jasper">Jasper</option> - <option value="Jazzberryjam">Jazzberryjam</option> - <option value="Jonquil">Jonquil</option> - <option value="Junebud">Junebud</option> - <option value="Junglegreen">Junglegreen</option> - <option value="Kellygreen">Kellygreen</option> - <option value="Khaki">Khaki</option> - <option value="KUCrimson">KUCrimson</option> - <option value="Languidlavender">Languidlavender</option> - <option value="Lapislazuli">Lapislazuli</option> - <option value="LaSalleGreen">LaSalleGreen</option> - <option value="LaserLemo">LaserLemo</option> - <option value="Lava">Lava</option> - <option value="Lavender">Lavender</option> - <option value="Lavenderblue">Lavenderblue</option> - <option value="Lavenderblush">Lavenderblush</option> - <option value="Lavendergray">Lavendergray</option> - <option value="Lavendermagenta">Lavendermagenta</option> - <option value="Lavendermist">Lavendermist</option> - <option value="Lavenderpink">Lavenderpink</option> - <option value="Lavenderpurple">Lavenderpurple</option> - <option value="Lavenderrose">Lavenderrose</option> - <option value="Lawngreen">Lawngren</option> - <option value="Lemon">Lemon</option> - <option value="Lemonchiffon">Lemonchiffon</option> - <option value="Lightapricot">Lightapricot</option> - <option value="Lightblue">Lightblue</option> - <option value="Lightbrown">Lightbrown</option> - <option value="Lightcarminepink">Lightcarminepink</option> - <option value="Lightcoral">Lightcoral</option> - <option value="Lightcornflowerblue">Lightcornflowerblue</option> - <option value="LightCrimson">LightCrimson</option> - <option value="Lightcyan">Lightcyan</option> - <option value="Lightfuchsiapink">Lightfuchsiapink</option> - <option value="Lightgoldenrodyellow">Lightgoldenrodyellow</option> - <option value="Lightgray">Lightgray</option> - <option value="Lightgreen">Lightgreen</option> - <option value="Lightkhaki">Lightkhaki</option> - <option value="Lightmauve">Lightmauve</option> - <option value="Lightpastelpurple">Lightpastelpurple</option> - <option value="Lightpink">Lightpink</option> - <option value="Lightsalmon">Lightsalmon</option> - <option value="Lightsalmonpink">Lightsalmonpink</option> - <option value="Lightseagreen">Lightseagreen</option> - <option value="Lightskyblue">Lightskyblue</option> - <option value="Lightslategray">Lightslategray</option> - <option value="Lighttaupe">Lighttaupe</option> - <option value="LightThulianpink">LightThulianpink</option> - <option value="Lightyellow">Lightyellow</option> - <option value="Lilac">Lilac</option> - <option value="Lime">Lime</option> - <option value="Limegreen">Limegreen</option> - <option value="Lincolngreen">Lincolngreen</option> - <option value="Linen">Linen</option> - <option value="Liver">Liver</option> - <option value="Lust">Lust</option> - <option value="Magenta">Magenta</option> - <option value="Magicmint">Magicmint</option> - <option value="Magnolia">Magnolia</option> - <option value="Mahogany">Mahogany</option> - <option value="MajorelleBlue">MajorelleBlue</option> - <option value="Malachite">Malachite</option> - <option value="Manatee">Manatee</option> - <option value="MangoTango">MangoTango</option> - <option value="Maroon">Maroon</option> - <option value="Mauve">Mauve</option> - <option value="Mauvelous">Mauvelous</option> - <option value="Mauvetaupe">Mauvetaupe</option> - <option value="Mayablue">Mayablue</option> - <option value="Meatbrown">Meatbrown</option> - <option value="Mediumaquamarine">Mediumaquamarine</option> - <option value="Mediumblue">Mediumblue</option> - <option value="Mediumcandyapplered">Mediumcandyapplered</option> - <option value="Mediumcarmine">Mediumcarmine</option> - <option value="Mediumchampagne">Mediumchampagne</option> - <option value="Mediumelectricblue">Mediumelectricblue</option> - <option value="Mediumjunglegreen">Mediumjunglegreen</option> - <option value="Mediumlavendermagenta">Mediumlavendermagenta</option> - <option value="Mediumorchid">Mediumorchid</option> - <option value="MediumPersianblue">MediumPersianblue</option> - <option value="Mediumpurple">Mediumpurple</option> - <option value="Mediumredviolet">Mediumredviolet</option> - <option value="Mediumseagreen">Mediumseagreen</option> - <option value="Atomictangerine">Atomictangerine</option> - <option value="Mediumslateblue">Mediumslateblue</option> - <option value="Mediumspringbud">Mediumspringbud</option> - <option value="Mediumspringgreen">Mediumspringgreen</option> - <option value="Mediumtaupe">Mediumtaupe</option> - <option value="Mediumtealblue">Mediumtealblue</option> - <option value="Mediumturquoise">Mediumturquoise</option> - <option value="Mediumvioletred">Mediumvioletred</option> - <option value="Melon">Melon</option> - <option value="Midnightblue">Midnightblue</option> - <option value="Midnightgreen">Midnightgreen</option> - <option value="Mikadoyellow">Mikadoyellow</option> - <option value="Mint">Mint</option> - <option value="Mintcream">Mintcream</option> - <option value="Mintgreen">Mintgreen</option> - <option value="Mistyrose">Mistyrose</option> - <option value="Moonstoneblue">Moonstoneblue</option> - <option value="Mordantred19">Mordantred19e</option> - <option value="Mossgreen">Mossgreen</option> - <option value="MountainMeadow">MountainMeadow</option> - <option value="Mountbattenpink">Mountbattenpink</option> - <option value="MSUGreen">MSUGreenl</option> - <option value="Midnight">Midnight</option> - <option value="Mulberry">Mulberry</option> - <option value="Mustard">Mustard</option> - <option value="Myrtle">Myrtle</option> - <option value="Nadeshikopink">Nadeshikopink</option> - <option value="Napiergreen">Napiergreen</option> - <option value="Navajowhite">Navajowhite</option> - <option value="Neonfuchsia">Neonfuchsia</option> - <option value="Neongreen">Neongreen</option> - <option value="Nonphotoblue">Nonphotoblue</option> - <option value="OceanBoatBlu">OceanBoatBlu</option> - <option value="Ochre">Ochre</option> - <option value="Oldgold">Oldgold</option> - <option value="Oldlace">Oldlace</option> - <option value="Oldlavender">Oldlavender</option> - <option value="Oldmauve">Oldmauve</option> - <option value="Oldrose">Oldrose</option> - <option value="Olive">Olive</option> - <option value="OliveDrab">OliveDrab</option> - <option value="OliveDrab7">OliveDrab7</option> - <option value="Olivine">Olivine</option> - <option value="Operamauve">Operamauve</option> - <option value="Orange">Orange</option> - <option value="Orangepeel">Orangepeel</option> - <option value="Orangered">Orangered</option> - <option value="Orchid">Orchid</option> - <option value="OUCrimsonRed">OUCrimsonRed</option> - <option value="OuterSpace">OuterSpace</option> - <option value="OutrageousOrange">OutrageousOrange</option> - <option value="OxfordBlue">OxfordBlue</option> - <option value="Pakistangreen">Pakistangreen</option> - <option value="Palatinateblue">Palatinateblue</option> - <option value="Palatinatepurple">Palatinatepurple</option> - <option value="Paleblue">Paleblue</option> - <option value="Palebrown">Palebrown</option> - <option value="Palecerulean">Palecerulean</option> - <option value="Palechestnut">Palechestnut</option> - <option value="Palecopper">Palecopper</option> - <option value="Palecornflowerblue">Palecornflowerblue</option> - <option value="Palegold">Palegolde</option> - <option value="Palegreen">Palegreen</option> - <option value="Palemagenta">Palemagenta</option> - <option value="Palepink">Palepink</option> - <option value="Paleredviolet">Paleredviolet</option> - <option value="Palerobineggblue">Palerobineggblue</option> - <option value="Palesilver">Palesilver</option> - <option value="Palespringbud">Palespringbud</option> - <option value="Paletaupe">Paletaupe</option> - <option value="Pansypurple">Pansypurple</option> - <option value="Papayawhip">Papayawhip</option> - <option value="Pastelblue">Pastelblue</option> - <option value="Pastelbrown">Pastelbrown</option> - <option value="Pastelgray">Pastelgray</option> - <option value="Pastelgreen">Pastelgreen</option> - <option value="Pastelmagenta">Pastelmagenta</option> - <option value="Pastelorange">Pastelorange</option> - <option value="Pastelpink">Pastelpink</option> - <option value="Pastelpurple">Pastelpurple</option> - <option value="Pastelred">Pastelred</option> - <option value="Pastelviolet">Pastelviolet</option> - <option value="Pastelyellow">Pastelyellow</option> - <option value="Paynesgray">Paynesgray</option> - <option value="Peach">Peach</option> - <option value="Peachorange">Peachorange</option> - <option value="Peachpuff">Peachpuff</option> - <option value="Peachyellow">Peachyellow</option> - <option value="Pear">Pear</option> - <option value="PearlAqua">PearlAqua</option> - <option value="Peridot">Peridot</option> - <option value="Persianblue">Persianblue</option> - <option value="Persiangreen">Persiangreen</option> - <option value="Persianindigo">Persianindigo</option> - <option value="Persianorange">Persianorange</option> - <option value="Persianpink">Persianpink</option> - <option value="Persianplum">Persianplum</option> - <option value="Persianred">Persianred</option> - <option value="Persianrose">Persianrose</option> - <option value="Persimmon">Persimmon</option> - <option value="Phlox">Phlox</option> - <option value="Phthaloblue">Phthaloblue</option> - <option value="Phthalogreen">Phthalogreen</option> - <option value="Piggypink">Piggypink</option> - <option value="Pinegreen">Pinegreen</option> - <option value="Pink">Pink</option> - <option value="Pinkpearl">Pinkpearl</option> - <option value="PinkSherbet">PinkSherbet</option> - <option value="Pistachio">Pistachio</option> - <option value="Platinum">Platinum</option> - <option value="Plum">Plum</option> - <option value="PortlandOrange">PortlandOrange</option> - <option value="Powderblue">Powderblue</option> - <option value="Princetonorange">Princetonorange</option> - <option value="Prussianblue">Prussianblue</option> - <option value="Puce">Puce</option> - <option value="Pumpkin">Pumpkin</option> - <option value="Purple">Purple</option> - <option value="PurpleHeart">PurpleHeart</option> - <option value="Purplemountainmajesty">Purplemountainmajesty</option> - <option value="Purplepizzazz">Purplepizzazz</option> - <option value="Purpletaupe">Purpletaupe</option> - <option value="Quartz">Quartz</option> - <option value="RadicalRed">RadicalRed</option> - <option value="Raspberry">Raspberry</option> - <option value="Raspberrypink">Raspberrypink</option> - <option value="Raspberryrose">Raspberryrose</option> - <option value="Rawumber">Rawumber</option> - <option value="Razzledazzlerose">Razzledazzlerose</option> - <option value="Razzmatazz">Razzmatazz</option> - <option value="Red">Red</option> - <option value="Redwood">Redwood</option> - <option value="Regalia">Regalia</option> - <option value="Richblack">Richblack</option> - <option value="Richbrilliantlavender">Richbrilliantlavender</option> - <option value="Richcarmine">Richcarmine</option> - <option value="Richelectricblue">Richelectricblue</option> - <option value="Richlavender">Richlavender</option> - <option value="Richlilac">Richlilac</option> - <option value="Richmaroon">Richmaroon</option> - <option value="Riflegreen">Riflegreen</option> - <option value="Robineggblue">Robineggblue</option> - <option value="Rosebonbon">Rosebonbon</option> - <option value="Roseebony">Roseebony</option> - <option value="Rosegold">Rosegold</option> - <option value="Rosepink">Rosepink</option> - <option value="Rosequartz">Rosequartz</option> - <option value="Rosetaupe">Rosetaupe</option> - <option value="Rosewood">Rosewood</option> - <option value="Rossocorsa">Rossocorsa</option> - <option value="Rosybrown">Rosybrown</option> - <option value="Royalazure">Royalazure</option> - <option value="Royalblue">Royalblue</option> - <option value="Royalfuchsia">Royalfuchsia</option> - <option value="Royalpurple">Royalpurple</option> - <option value="Ruby">Ruby</option> - <option value="Ruddy">Ruddy</option> - <option value="Ruddybrown">Ruddybrown</option> - <option value="Ruddypink">Ruddypink</option> - <option value="Rufous">Rufouse</option> - <option value="Russet">Russet</option> - <option value="Rust">Rust</option> - <option value="SacramentoStategreen">SacramentoStategreen</option> - <option value="Saddlebrown">Saddlebrown</option> - <option value="Safetyorange">Safetyorange</option> - <option value="Saffron">Saffron</option> - <option value="Salmon">Salmon</option> - <option value="Salmonpink">Salmonpink</option> - <option value="Sandstorm">Sandstorm</option> - <option value="Sandybrown">Sandybrown</option> - <option value="Sangria">Sangria</option> - <option value="Sapgreen">Sapgreen</option> - <option value="Sapphire">Sapphire</option> - <option value="Satinsheengold">Satinsheengold</option> - <option value="Scarlet">Scarlet</option> - <option value="Schoolbusyellow">Schoolbusyellow</option> - <option value="ScreaminGreen">ScreaminGreen</option> - <option value="Seagreen">Seagreen</option> - <option value="Sealbrown">Sealbrown</option> - <option value="Seashell">Seashell</option> - <option value="Selectiveyellow">Selectiveyellow</option> - <option value="Sepia">Sepia</option> - <option value="Shadow">Shadow</option> - <option value="Shamrockgreen">Shamrockgreen</option> - <option value="Shockingpink">Shockingpink</option> - <option value="Sienna">Sienna</option> - <option value="Silver">Silver</option> - <option value="Sinopia">Sinopia</option> - <option value="Skobeloff">Skobeloff</option> - <option value="Skyblue">Skyblue</option> - <option value="Skymagenta">Skymagenta</option> - <option value="Slateblue">Slateblue</option> - <option value="Slategray">Slategrayh</option> - <option value="Smokeytopaz">Smokeytopaz</option> - <option value="Smokyblack">Smokyblack</option> - <option value="Snow">Snow</option> - <option value="SpiroDiscoBall">SpiroDiscoBalld</option> - <option value="Splashedwhite">Splashedwhite</option> - <option value="Springbud">Springbud</option> - <option value="Steelblue">Steelblue</option> - <option value="St.Patricksblue">St.Patricksblue</option> - <option value="Straw">Straw</option> - <option value="Tan">Tan</option> - <option value="Tangelo">Tangelo</option> - <option value="Tangerine">Tangerine</option> - <option value="Tangerineyellow">Tangerineyellow</option> - <option value="Taupegray">Taupegray</option> - <option value="Teagreen">Teagreen</option> - <option value="Teal">Teal</option> - <option value="Tealblue">Tealblue</option> - <option value="Tealgreen">Tealgreen</option> - <option value="Tenné">Tenné</option> - <option value="Terracotta">Terracotta</option> - <option value="Thistle">Thistle</option> - <option value="Thulianpink">Thulianpink</option> - <option value="TickleMePink">TickleMePink</option> - <option value="TiffanyBlue">TiffanyBlue</option> - <option value="Tigerseye">Tigerseye</option> - <option value="Timberwolf">Timberwolf</option> - <option value="Titaniumyellow">Titaniumyellow</option> - <option value="Tomato">Tomato</option> - <option value="Toolbox">Toolbox</option> - <option value="Topaz">Topaz</option> - <option value="Tractorred">Tractorred</option> - <option value="Tropicalrainforest">Tropicalrainforest</option> - <option value="TrueBlue">TrueBlue</option> - <option value="TuftsBlue">TuftsBlue</option> - <option value="Tumbleweed">Tumbleweed</option> - <option value="Turkishrose">Turkishrose</option> - <option value="Turquoise">Turquoise</option> - <option value="Turquoiseblue">Turquoiseblue</option> - <option value="Turquoisegreen">Turquoisegreen</option> - <option value="Tuscanred">Tuscanred</option> - <option value="Twilightlavender">Twilightlavender</option> - <option value="Tyrianpurple">Tyrianpurple</option> - <option value="UAblue">UAblue</option> - <option value="UAred">UAred</option> - <option value="Ube">Ube</option> - <option value="UCLABlue">UCLABlue</option> - <option value="UCLAGold">UCLAGold</option> - <option value="UFOGreen">UFOGreen</option> - <option value="Ultramarine">Ultramarine</option> - <option value="Ultramarineblue">Ultramarineblue</option> - <option value="Ultrapink">Ultrapink</option> - <option value="UnitedNationsblue">UnitedNationsblue</option> - <option value="UniversityofCaliforniaGold">UniversityofCaliforniaGold</option> - <option value="UnmellowYellow">UnmellowYellow</option> - <option value="UPMaroon">UPMaroon</option> - <option value="Upsdellred">Upsdellred</option> - <option value="Urobilin">Urobilin</option> - <option value="UtahCrimson">UtahCrimson</option> - <option value="Vegasgold">Vegasgold</option> - <option value="Venetianred">Venetianred</option> - <option value="Verdigris">Verdigris</option> - <option value="Veronica">Veronica</option> - <option value="Violet">Violet</option> - <option value="Viridian">Viridian</option> - <option value="Vividauburn">Vividauburn</option> - <option value="Vividburgundy">Vividburgundy</option> - <option value="Vividceris">Vividceris</option> - <option value="Vividtangerine">Vividtangerine</option> - <option value="Vividviolet">Vividviolet</option> - <option value="Warmblack">Warmblack</option> - <option value="Wenge">Wenge</option> - <option value="Wheat">Wheat</option> - <option value="White">White</option> - <option value="Whitesmoke">Whitesmoke</option> - <option value="Wildblueyonder">Wildblueyonder</option> - <option value="WildStrawberry">WildStrawberry</option> - <option value="WildWatermelon">WildWatermelon</option> - <option value="Wine">Wine</option> - <option value="Wisteria">Wisteria</option> - <option value="Xanadu">Xanadu</option> - <option value="YaleBlue">YaleBlue</option> - <option value="Yellow">Yellow</option> - <option value="Yellowgreen">Yellowgreen</option> - <option value="YellowOrange">YellowOrange</option> - <option value="Zaffre">Zaffre</option> - <option value="Zinnwalditebrown">Zinnwalditebrown</option> - </param> + <param type="boolean" name="label" checked="true" label="Use Labels"/> + <param type="float" name="cutoff" label="SAINT Score Cutoff" help="Select a value between 0 and 1 written like 0.8." value="0.8"/> + <param format="txt" name="inc_file" type="data" label="List of Uniprot IDs to Include" optional="true"/> + <param format="txt" name="exc_file" type="data" label="List of Uniprot IDs to Exclude" optional="true"/> </inputs> - <outputs> - <data format="png" name="outfile" label="Bubble Plot" /> + <outputs> + <data format="txt" name="outfile" label="Outfile"/> + <data format="png" name="NSAF_zoom" label="Zoom NSAF" /> + <data format="png" name="SAINT_zoom" label="Zoom SAINT" /> + <data format="png" name="NSAF" label="NSAF" /> + <data format="png" name="SAINT" label="SAINT" /> </outputs> <stdio> - <regex match="ValueError: 'PreyGene' is not in list" - source="stdout" - level="fatal" - description="Error: Check Input file."/> - <regex match="Error|error" - source="stdout" - level="fatal" - description="Unknown error"/> - <regex match="Error|error" - source="stderr" + <regex match="error" + source="stdout" level="fatal" description="Unknown error"/> </stdio> @@ -1435,96 +40,89 @@ </test> </tests> <help> -Bubble Graph Generator -^^^^^^^^^^^^^^^^^^^^^^ +Post-processing: +Once SAINTexpress has been run, APOSTL is able to read the resulting "list.txt" file. Fromhere APOSTL does a number of things: -This Bubble Graph Generator is a static version of the APOSTL interactive affinity proteomics analysis -software developed to reformat affinity proteomics data (both spectral counting and MS1) for input -into the SAINTexpress statistical package and to visualize the output(s). APOSTL was developed at -H. Lee Moffitt Cancer Center and Research Institute and distributed under a GNU General Public License (GPL). +APOSTL calculates NSAF values for each prey based on the average spectra observed for each bait --------------- +OPTIONAL: APOSTL calculates the probability of a specific interaction based on prey revalence in the CRAPome + +Bubble graphs are generated for each bait where: -**1) SAINT Output File** +- x axis is the natural log of the NSAF values -SAINTexpress generated *list.txt* file. +- y axis is the observed log2 fold change (as compared to control) - **Note:** Prey IDs must be in Uniprot/Swissprot format (e.g. - "EGFR\_HUMAN" or "P00533"). +- bubble radius is proportional to the average observed spectra -**2) Prey File** +OPTIONAL: bubble color corresponds to the CRAPome probability of a specific interaction in which an 80% cutoff is applied where prey with less than 80% are colored tan -Please specify a *Prey* file for Bubble Graph creation. A *Prey* file -should contain three columns: prey (protein) name, prey amino acid -length, and prey gene name (no header). +APOSTL queries ConsensusPathDB for protein-protein interactions within your data and then formats the resulting network for simple cytoscape import using the "import network from file" option. -**3) CRAPome File** +INPUTS: + +List File: -Please specify an *CRAPome* file for Bubble Graph creation. An *CRAPome* -file should contain five columns: IP name, Mapped Gene Symbol, Number of -Experiments (ratio), and Average spectral counts, and Max spectral counts. +- SAINTexpress generated "list.txt" file -**4) Interactions File** +Prey File: + +- SAINT pre-processing generated "prey.txt" file used to run SAINTexpress -Please specify an *Inter* file for Bubble Graph creation. An *Inter* -file should contain four columns: IP name, bait name, prey name, and -spectral counts or intensity values, depending on the mode of -quantification. +Crapome File: -**5) X Axis Label** +- raw output from Crapome Workflow 1 query (http://www.crapome.org) + +Color: -Select the value to be used as the X axis in the Bubble Graph. - -**6) Y Axis Label** +- Specify the color of the bubbles within the graph. -Selct the value to be used as the Y axis in the Bubble Graph. +- If "crapome" is chosen and 'crapome' file is specified, bubbles will be color based on crapome specificity -**7) Bubble Size** +Use labels: -Select the value to size the bubbles in the Bubble Graph. The "fixed" -option will make all the bubbles the same size +- Adds gene name labels to bubbles within the "zoomed in" graphs +SAINT Score Cutoff: -**8) Color** +- Choose Saintscore cutoff (between 0-1) to be used for filtering the "zoomed in" graphs (default = 0.8) -Crapome will color the bubbles acooring to their likelyhood of a good -interaction. Fixed will make all the bubbles one color (must be used if no-crapome -file is provided). +- Also used for filtering during the generation of the cytoscape network -**9) SAINT Score Cutoff** +Species: + +- Human, mouse, or yeast -SaintScore filter in range 0-1 (default 0.8) +Interaction Confidence: -**10) Fold Change Cutoff** +- Interaction confidence value (0-1) used to filter the interactions with the ConsensusPathDB database -Fold Change filter in range -Inf to Inf (default 0) +- Suggestions: -**11) NSAF Score Cutoff** +* low: 0 -NSAF Score filter in range -Inf to Inf (default 0) +* medium: 0.5 -**12) Plot Theme** +* high: 0.7 -Select theme to be used when creating Bubble Graph. +* very high: 0.9 -**13) Label Type** +OUTPUTS: -Select the type of labeling: no labels, label points greater than CRAPomePCT cutoff, and -all bubbles labeled. +Bubble Graphs: -**14) Label Color** +- Unfiltered Data: -Select label color. +* NSAF v. Log2(FoldChange) -**15) Bubble Color** +* SAINTscore v. Log2(FoldChange) -Select color of Bubble interior. If *Color* is set to *crapome* this will act as the color of CRAPomePCT > 80. If *Color* is set to *fixed* this will be the bubble color. +- Filtered by SAINT Score -**16) Outline Color** +* NSAF v. Log2(FoldChange) -Select the bubble outline color. - -**17) Crapome Filter Color** +* SAINTscore v. Log2(FoldChange) -Select color of CRAPome filtering. If *Color* is set to *crapome* this will act as the color of CRAPomePCT < 80. If *Color* is set to *fixed* this will not be used. - </help> +Output.txt +- SAINTexpress "list.txt" output with additional columns that were used during the analysis + </help> </tool>