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APOSTL_Static_Bubblegraph_Generator.xml |
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| diff -r f0901a52b310 -r ed4d14e83f44 APOSTL_Static_Bubblegraph_Generator.xml --- 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 |
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| b'@@ -1,1429 +1,34 @@\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/\r\n- </command>\r\n- <requirements>\r\n- <requirement type="set_environment">INSTALL_RUN_PATH</requirement>\r\n- </requirements>\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 </command>\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="lnNSAF">ln(NSAF)</option>\r\n- <option value="SpecSum">SpecSum</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="lnNSAF">ln(NSAF)</option>\r\n- <option value="SpecSum">SpecSum</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="fixed">fixed</option> \r\n- <option value="lnNSAF">ln(NSAF)</option>\r\n- <option value="SpecSum">SpecSum</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+ <param name="color" type="select" label="Color" optional="true">\r\n <option value="crapome">Crapome</option>\r\n- <option value="fixed">fixed</option>\r\n- </param>\r\n- <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"/>\r\n- <param type="integer" name="FC_cutoff" label="Fold Change Cutoff" help="Select a value between -Inf and Inf." value="0"/>\r\n- <param type="integer" name="NS_cutoff" label="NSAF Score Cutoff" help="Select a value between -Inf and Inf." value="0"/>\r\n- <param name="theme" type="select" label="Plot Theme" >\r\n- <option value="Default">Default</option>\r\n- <option value="b/w">b/w</option>\r\n- <option value="minimal">minimal</option>\r\n- <option value="classic">classic</option>\r\n- <option value="dark">dark</option>\r\n- <option value="linedraw">linedraw</option>\r\n- </param>\r\n- <param name="label" type="select" label="Label Type" >\r\n- <option value="none">none</option>\r\n- <option value="cutoff">cutoff</option>\r\n- <option value="all">all</option>\r\n- </param>\r\n- <param name="label_color" type="select" label="Label Color" >\r\n- <option value="black">Black</option>\r\n- <option value="white">White</option>\r\n+ <option value="red">Red</option>\r\n+ <option value'..b'.\r\n+- bubble radius is proportional to the average observed spectra\r\n \r\n-**2) Prey File**\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-Please specify a *Prey* file for Bubble Graph creation. A *Prey* file\r\n-should contain three columns: prey (protein) name, prey amino acid\r\n-length, and prey gene name (no header).\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-**3) CRAPome File**\r\n+INPUTS:\r\n+\r\n+List File: \r\n \r\n-Please specify an *CRAPome* file for Bubble Graph creation. An *CRAPome*\r\n-file should contain five columns: IP name, Mapped Gene Symbol, Number of \r\n-Experiments (ratio), and Average spectral counts, and Max spectral counts.\r\n+- SAINTexpress generated "list.txt" file\r\n \r\n-**4) Interactions File**\r\n+Prey File:\r\n+\r\n+- SAINT pre-processing generated "prey.txt" file used to run SAINTexpress\r\n \r\n-Please specify an *Inter* file for Bubble Graph creation. An *Inter*\r\n-file should contain four columns: IP name, bait name, prey name, and\r\n-spectral counts or intensity values, depending on the mode of\r\n-quantification.\r\n+Crapome File:\r\n \r\n-**5) X Axis Label**\r\n+- raw output from Crapome Workflow 1 query (http://www.crapome.org)\r\n+\r\n+Color:\r\n \r\n-Select the value to be used as the X axis in the Bubble Graph.\r\n-\r\n-**6) Y Axis Label**\r\n+- Specify the color of the bubbles within the graph.\r\n \r\n-Selct the value to be used as the Y axis in the Bubble Graph.\r\n+- If "crapome" is chosen and \'crapome\' file is specified, bubbles will be color based on crapome specificity\r\n \r\n-**7) Bubble Size**\r\n+Use labels:\r\n \r\n-Select the value to size the bubbles in the Bubble Graph. The "fixed"\r\n-option will make all the bubbles the same size\r\n+- Adds gene name labels to bubbles within the "zoomed in" graphs\r\n+SAINT Score Cutoff:\r\n \r\n-**8) Color**\r\n+- Choose Saintscore cutoff (between 0-1) to be used for filtering the "zoomed in" graphs (default = 0.8)\r\n \r\n-Crapome will color the bubbles acooring to their likelyhood of a good\r\n-interaction. Fixed will make all the bubbles one color (must be used if no-crapome \r\n-file is provided).\r\n+- Also used for filtering during the generation of the cytoscape network\r\n \r\n-**9) SAINT Score Cutoff**\r\n+Species:\r\n+\r\n+- Human, mouse, or yeast\r\n \r\n-SaintScore filter in range 0-1 (default 0.8)\r\n+Interaction Confidence:\r\n \r\n-**10) Fold Change Cutoff**\r\n+- Interaction confidence value (0-1) used to filter the interactions with the ConsensusPathDB database\r\n \r\n-Fold Change filter in range -Inf to Inf (default 0)\r\n+- Suggestions:\r\n \r\n-**11) NSAF Score Cutoff**\r\n+* low: 0\r\n \r\n-NSAF Score filter in range -Inf to Inf (default 0)\r\n+* medium: 0.5\r\n \r\n-**12) Plot Theme**\r\n+* high: 0.7\r\n \r\n-Select theme to be used when creating Bubble Graph.\r\n+* very high: 0.9\r\n \r\n-**13) Label Type**\r\n+OUTPUTS:\r\n \r\n-Select the type of labeling: no labels, label points greater than CRAPomePCT cutoff, and \r\n-all bubbles labeled.\r\n+Bubble Graphs:\r\n \r\n-**14) Label Color**\r\n+- Unfiltered Data:\r\n \r\n-Select label color.\r\n+* NSAF v. Log2(FoldChange)\r\n \r\n-**15) Bubble Color**\r\n+* SAINTscore v. Log2(FoldChange)\r\n \r\n-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.\r\n+- Filtered by SAINT Score\r\n \r\n-**16) Outline Color**\r\n+* NSAF v. Log2(FoldChange)\r\n \r\n-Select the bubble outline color.\r\n-\r\n-**17) Crapome Filter Color**\r\n+* SAINTscore v. Log2(FoldChange) \r\n \r\n-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.\r\n- </help>\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' |