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APOSTL_Static_Bubblegraph_Generator.xml |
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| diff -r 0a740024e014 -r aa0debcd27be APOSTL_Static_Bubblegraph_Generator.xml --- a/APOSTL_Static_Bubblegraph_Generator.xml Wed May 11 11:14:37 2016 -0400 +++ b/APOSTL_Static_Bubblegraph_Generator.xml Wed May 11 11:14:45 2016 -0400 |
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| b'@@ -1,715 +1,43 @@\n <tool id="APOSTL_Static_Bubblegraph_Generator" name="APOSTL Static Bubblegraph Generator">\r\n <description></description>\r\n- <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>\r\n+ <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/\r\n+ </command>\r\n <requirements>\r\n <requirement type="set_environment">INSTALL_RUN_PATH</requirement>\r\n </requirements>\r\n <inputs>\r\n- <param type="select" name="type" label="MaxQuant or Scaffold">\r\n- <option value="MQ">MaxQuant</option>\r\n- <option value="SC">Scaffold</option> \r\n- </param>\r\n <param format="txt" name="list_file" type="data" label="List File"/>\r\n <param format="txt" name="prey_file" type="data" label="Prey File"/>\r\n <param format="txt" name="crapome" type="data" label="Crapome File" optional="true"/>\r\n <param format="txt" name="inter" type="data" label="Inter File"/>\r\n <param name="main_x" type="select" label="X Axis" >\r\n- <option value="ln(NSAF)">ln(NSAF)</option>\r\n+ <option value="lnNSAF">ln(NSAF)</option>\r\n <option value="SpecSum">SpecSum</option>\r\n- <option value="log2(FoldChange)">log2(FoldChange)</option>\r\n+ <option value="log2FoldChange">log2(FoldChange)</option>\r\n <option value="SaintScore">SaintScore</option>\r\n <option value="logOddsScore">logOddsScore</option>\r\n <option value="NSAFScore">NSAFScore</option>\r\n </param>\r\n <param name="main_y" type="select" label="Y Axis" >\r\n- <option value="ln(NSAF)">ln(NSAF)</option>\r\n+ <option value="lnNSAF">ln(NSAF)</option>\r\n <option value="SpecSum">SpecSum</option>\r\n- <option value="log2(FoldChange)">log2(FoldChange)</option>\r\n+ <option value="log2FoldChange">log2(FoldChange)</option>\r\n <option value="SaintScore">SaintScore</option>\r\n <option value="logOddsScore">logOddsScore</option>\r\n <option value="NSAFScore">NSAFScore</option>\r\n </param>\r\n <param name="size_id" type="select" label="Bubble Size" >\r\n- <option value="ln(NSAF)">ln(NSAF)</option>\r\n+ <option value="fixed">fixed</option> \r\n+ <option value="lnNSAF">ln(NSAF)</option>\r\n <option value="SpecSum">SpecSum</option>\r\n- <option value="log2(FoldChange)">log2(FoldChange)</option>\r\n+ <option value="log2FoldChange">log2(FoldChange)</option>\r\n <option value="SaintScore">SaintScore</option>\r\n <option value="logOddsScore">logOddsScore</option>\r\n <option value="NSAFScore">NSAFScore</option>\r\n </param>\r\n <param name="color" type="select" label="Color" >\r\n <option value="crapome">Crapome</option>\r\n- <option value="Air Force blue">Air Force blue</option>\r\n- <option value="Alice blue">Alice blue</option>\r\n- <option value="Alizarin crimson">Alizarin crimson</option>\r\n- <option value="Almond">Almond</option>\r\n- <option value="Amaranth">Amaranth</option>\r\n- <option value="Amber">Amber</option>\r\n- <option value="American rose">American rose</option>\r\n- <option value="Amethyst">Amethyst</option>\r\n- <option value="Android Green">Android Green</option>\r\n- <option value="Air Force blue">Anti flash white</option>\r\n- <option value="Antique fuchsia">Antique fuchsia</option>\r\n- <option value="Antique white">Antique white</option>\r\n- <option value="Ao">Ao</option>\r\n- <option value="Apple green">Apple green</option>\r\n- <option value="Apricot">Apricot</option>\r\n- <option value="Aqua">A'..b'/option>\r\n- <option value="UFO Green">UFO Green</option>\r\n+ <option value="UCLABlue">UCLABlue</option>\r\n+ <option value="UCLAGold">UCLAGold</option>\r\n+ <option value="UFOGreen">UFOGreen</option>\r\n <option value="Ultramarine">Ultramarine</option>\r\n- <option value="Ultramarine blue">Ultramarine blue</option>\r\n- <option value="Ultra pink">Ultra pink</option>\r\n- <option value="United Nations blue">United Nations blue</option>\r\n- <option value="University of California Gold">University of California Gold</option>\r\n- <option value="Unmellow Yellow">Unmellow Yellow</option>\r\n- <option value="UP Maroon">UP Maroon</option>\r\n- <option value="Upsdell red">Upsdell red</option>\r\n+ <option value="Ultramarineblue">Ultramarineblue</option>\r\n+ <option value="Ultrapink">Ultrapink</option>\r\n+ <option value="UnitedNationsblue">UnitedNationsblue</option>\r\n+ <option value="UniversityofCaliforniaGold">UniversityofCaliforniaGold</option>\r\n+ <option value="UnmellowYellow">UnmellowYellow</option>\r\n+ <option value="UPMaroon">UPMaroon</option>\r\n+ <option value="Upsdellred">Upsdellred</option>\r\n <option value="Urobilin">Urobilin</option>\r\n- <option value="Utah Crimson">Utah Crimson</option>\r\n- <option value="Vegas gold">Vegas gold</option>\r\n- <option value="Venetian red">Venetian red</option>\r\n+ <option value="UtahCrimson">UtahCrimson</option>\r\n+ <option value="Vegasgold">Vegasgold</option>\r\n+ <option value="Venetianred">Venetianred</option>\r\n <option value="Verdigris">Verdigris</option>\r\n <option value="Veronica">Veronica</option>\r\n <option value="Violet">Violet</option>\r\n <option value="Viridian">Viridian</option>\r\n- <option value="Vivid auburn">Vivid auburn</option>\r\n- <option value="Vivid burgundy">Vivid burgundy</option>\r\n- <option value="Vivid ceris">Vivid ceris</option>\r\n- <option value="Vivid tangerine">Vivid tangerine</option>\r\n- <option value="Vivid violet">Vivid violet</option>\r\n- <option value="Warm black">Warm black</option>\r\n+ <option value="Vividauburn">Vividauburn</option>\r\n+ <option value="Vividburgundy">Vividburgundy</option>\r\n+ <option value="Vividceris">Vividceris</option>\r\n+ <option value="Vividtangerine">Vividtangerine</option>\r\n+ <option value="Vividviolet">Vividviolet</option>\r\n+ <option value="Warmblack">Warmblack</option>\r\n <option value="Wenge">Wenge</option>\r\n <option value="Wheat">Wheat</option>\r\n <option value="White">White</option>\r\n- <option value="White smoke">White smoke</option>\r\n- <option value="Wild blue yonder">Wild blue yonder</option>\r\n- <option value="Wild Strawberry">Wild Strawberry</option>\r\n- <option value="Wild Watermelon">Wild Watermelon</option>\r\n+ <option value="Whitesmoke">Whitesmoke</option>\r\n+ <option value="Wildblueyonder">Wildblueyonder</option>\r\n+ <option value="WildStrawberry">WildStrawberry</option>\r\n+ <option value="WildWatermelon">WildWatermelon</option>\r\n <option value="Wine">Wine</option>\r\n <option value="Wisteria">Wisteria</option>\r\n <option value="Xanadu">Xanadu</option>\r\n- <option value="Yale Blue">Yale Blue</option>\r\n+ <option value="YaleBlue">YaleBlue</option>\r\n <option value="Yellow">Yellow</option>\r\n- <option value="Yellow green">Yellow green</option>\r\n- <option value="Yellow Orange">Yellow Orange</option>\r\n+ <option value="Yellowgreen">Yellowgreen</option>\r\n+ <option value="YellowOrange">YellowOrange</option>\r\n <option value="Zaffre">Zaffre</option>\r\n- <option value="Zinnwaldite brown">Zinnwaldite brown</option>\r\n+ <option value="Zinnwalditebrown">Zinnwalditebrown</option>\r\n </param>\r\n </inputs>\r\n <outputs> \r\n' |