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APOSTL_Static_Bubblegraph_Generator.xml |
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| diff -r 8f463e2a34d5 -r f3fcab0e9edd APOSTL_Static_Bubblegraph_Generator.xml --- a/APOSTL_Static_Bubblegraph_Generator.xml Wed May 11 10:59:06 2016 -0400 +++ b/APOSTL_Static_Bubblegraph_Generator.xml Wed May 11 10:59:16 2016 -0400 |
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| b'@@ -1,6 +1,6 @@\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 $color $label $cutoff $type $inc_file $exc_file $outfile $NSAF_zoom $SAINT_zoom $SAINT $NSAF \\$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/</command>\r\n <requirements>\r\n <requirement type="set_environment">INSTALL_RUN_PATH</requirement>\r\n </requirements>\r\n@@ -12,26 +12,2094 @@\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 name="color" type="select" label="Color" 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="SpecSum">SpecSum</option>\r\n+ <option value="log2(FoldChange)">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="SpecSum">SpecSum</option>\r\n+ <option value="log2(FoldChange)">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="SpecSum">SpecSum</option>\r\n+ <option value="log2(FoldChange)">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="red">Red</option>\r\n- <option value="blue">Blue</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">Aqua</option>\r\n+ <option value="Amber">Amber</option>\r\n+ <option value="Aquamarine">Aquamarine</option>\r\n+ <option value="Amethyst">Amethyst</option>\r\n+ <option value="Army green">Army green</option>\r\n+ <option value="Arsenic">Arsenic</option>\r\n+ <option value="Arylide yellow">Arylide yellow</option>\r\n+ <option value="Ash gray">Ash gray</option>\r\n+ <option value="Asparagus">Asparagus</option>\r\n+ <option valu'..b'>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="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="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="Zaffre">Zaffre</option>\r\n+ <option value="Zinnwaldite brown">Zinnwaldite brown</option>\r\n+ </param>\r\n </inputs>\r\n- <outputs>\r\n- <data format="txt" name="outfile" label="Outfile"/> \r\n- <data format="png" name="NSAF_zoom" label="Zoom NSAF" />\r\n- <data format="png" name="SAINT_zoom" label="Zoom SAINT" />\r\n- <data format="png" name="NSAF" label="NSAF" />\r\n- <data format="png" name="SAINT" label="SAINT" />\r\n+ <outputs> \r\n+ <data format="png" name="outfile" label="Bubble Plot" />\r\n </outputs>\r\n <stdio>\r\n- <regex match="error"\r\n-\t source="stdout"\r\n+ <regex match="ValueError: \'PreyGene\' is not in list"\r\n+ source="stdout"\r\n+ level="fatal"\r\n+ description="Error: Check Input file."/>\r\n+ <regex match="Error|error"\r\n+ source="stdout"\r\n+ level="fatal"\r\n+ description="Unknown error"/>\r\n+ <regex match="Error|error"\r\n+ source="stderr"\r\n level="fatal"\r\n description="Unknown error"/>\r\n </stdio> \r\n@@ -43,89 +2111,5 @@\n </test>\r\n </tests>\r\n <help>\r\n-Post-processing:\r\n-Once SAINTexpress has been run, APOSTL is able to read the resulting "list.txt" file. Fromhere APOSTL does a number of things:\r\n-\r\n-APOSTL calculates NSAF values for each prey based on the average spectra observed for each bait\r\n-\r\n-OPTIONAL: APOSTL calculates the probability of a specific interaction based on prey revalence in the CRAPome \r\n-\r\n-Bubble graphs are generated for each bait where:\r\n-\r\n-- x axis is the natural log of the NSAF values\r\n-\r\n-- y axis is the observed log2 fold change (as compared to control)\r\n-\r\n-- bubble radius is proportional to the average observed spectra\r\n-\r\n-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\r\n-\r\n-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.\r\n-\r\n-INPUTS:\r\n-\r\n-List File: \r\n-\r\n-- SAINTexpress generated "list.txt" file\r\n-\r\n-Prey File:\r\n-\r\n-- SAINT pre-processing generated "prey.txt" file used to run SAINTexpress\r\n-\r\n-Crapome File:\r\n-\r\n-- raw output from Crapome Workflow 1 query (http://www.crapome.org)\r\n-\r\n-Color:\r\n-\r\n-- Specify the color of the bubbles within the graph.\r\n-\r\n-- If "crapome" is chosen and \'crapome\' file is specified, bubbles will be color based on crapome specificity\r\n-\r\n-Use labels:\r\n-\r\n-- Adds gene name labels to bubbles within the "zoomed in" graphs\r\n-SAINT Score Cutoff:\r\n-\r\n-- Choose Saintscore cutoff (between 0-1) to be used for filtering the "zoomed in" graphs (default = 0.8)\r\n-\r\n-- Also used for filtering during the generation of the cytoscape network\r\n-\r\n-Species:\r\n-\r\n-- Human, mouse, or yeast\r\n-\r\n-Interaction Confidence:\r\n-\r\n-- Interaction confidence value (0-1) used to filter the interactions with the ConsensusPathDB database\r\n-\r\n-- Suggestions:\r\n-\r\n-* low: 0\r\n-\r\n-* medium: 0.5\r\n-\r\n-* high: 0.7\r\n-\r\n-* very high: 0.9\r\n-\r\n-OUTPUTS:\r\n-\r\n-Bubble Graphs:\r\n-\r\n-- Unfiltered Data:\r\n-\r\n-* NSAF v. Log2(FoldChange)\r\n-\r\n-* SAINTscore v. Log2(FoldChange)\r\n-\r\n-- Filtered by SAINT Score\r\n-\r\n-* NSAF v. Log2(FoldChange)\r\n-\r\n-* SAINTscore v. Log2(FoldChange) \r\n-\r\n-Output.txt\r\n-- SAINTexpress "list.txt" output with additional columns that were used during the analysis\r\n </help>\r\n </tool>\r\n' |