--- a/Bubblebeam_For_SAINT_wrapper.py	Thu Nov 19 11:15:58 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-import os 
-import sys
-import time
-
-
-list_file = sys.argv[1]
-prey_file = sys.argv[2]
-crapome = sys.argv[3]
-color = sys.argv[4]
-label = sys.argv[5]
-cutoff = sys.argv[6]
-mq_sc = sys.argv[7]
-inc_file = sys.argv[8]
-exc_file = sys.argv[9]
-output_file_name = sys.argv[10]
-bub_zoom_NSAF = sys.argv[11]
-bub_zoom_SAINT =sys.argv[12]
-bub_SAINT = sys.argv[13]
-bub_NSAF = sys.argv[14]
-ins_path =sys.argv[15]
-
-if crapome == "None":
-	crapome = "FALSE"
-
-
-if label == "false":
-	label = "FALSE"
-elif label == "true":
-	label = "TRUE" 
-
-cmd = r"Rscript "+ str(ins_path) + r"/bubbles_v9_NSAF_natural_log.R " + str(list_file) + r" " + str(prey_file) + r" " + str(crapome) + r" " + str(color) + r" " + str(label) + r" " + str(cutoff) + r" " + str(mq_sc) + r" " + str(inc_file) + r" " + str(exc_file)
-os.system(cmd)
-time.sleep(3)
-
-open('./output.txt')
-os.rename('output.txt', str(output_file_name))
-
-open('./bubble_zoom_NSAF.png')
-os.rename('bubble_zoom_NSAF.png', str(bub_zoom_NSAF))
-
-open('./bubble_zoom_SAINT.png')
-os.rename('bubble_zoom_SAINT.png', str(bub_zoom_SAINT))
-
-open('./bubble_SAINT.png')
-os.rename('bubble_SAINT.png', str(bub_SAINT))
-
-open('./bubble_NSAF.png')
-os.rename('bubble_NSAF.png', str(bub_NSAF))
-

--- a/Bubblebeam_For_SAINT_wrapper.xml	Thu Nov 19 11:15:58 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,131 +0,0 @@
-<tool id="Bubblebeam_For_SAINT" name="Bubblebeam For SAINT">
-  <description></description>
-  <command interpreter="python">Bubblebeam_For_SAINT_wrapper.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>
-  <requirements>
-    <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
-  </requirements>
-  <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 name="color" type="select" label="Color">
-        <option value="crapome">Crapome</option>
-        <option value="red">Red</option>
-        <option value="blue">Blue</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 Include" optional="true"/>
-  </inputs>
-  <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="error"
-	   source="stdout"
-           level="fatal"
-           description="Unknown error"/>
-  </stdio> 
-
-  <tests>
-    <test>
-      <param name="input" value="fa_gc_content_input.fa"/>
-      <output name="out_file1" file="fa_gc_content_output.txt"/>
-    </test>
-  </tests>
-  <help>
-Post-processing:
-Once SAINTexpress has been run, APOSTL is able to read the resulting "list.txt" file. Fromhere APOSTL does a number of things:
-
-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:
-
-- x axis is the natural log of the NSAF values
-
-- y axis is the observed log2 fold change (as compared to control)
-
-- bubble radius is proportional to the average observed spectra
-
-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
-
-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.
-
-INPUTS:
-
-List File: 
-
-- SAINTexpress generated "list.txt" file
-
-Prey File:
-
-- SAINT pre-processing generated "prey.txt" file used to run SAINTexpress
-
-Crapome File:
-
-- raw output from Crapome Workflow 1 query (http://www.crapome.org)
-
-Color:
-
-- Specify the color of the bubbles within the graph.
-
-- If "crapome" is chosen and 'crapome' file is specified, bubbles will be color based on crapome specificity
-
-Use labels:
-
-- Adds gene name labels to bubbles within the "zoomed in" graphs
-SAINT Score Cutoff:
-
-- Choose Saintscore cutoff (between 0-1) to be used for filtering the "zoomed in" graphs (default = 0.8)
-
-- Also used for filtering during the generation of the cytoscape network
-
-Species:
-
-- Human, mouse, or yeast
-
-Interaction Confidence:
-
-- Interaction confidence value (0-1) used to filter the interactions with the ConsensusPathDB database
-
-- Suggestions:
-
-* low: 0
-
-* medium: 0.5
-
-* high: 0.7
-
-* very high: 0.9
-
-OUTPUTS:
-
-Bubble Graphs:
-
-- Unfiltered Data:
-
-* NSAF v. Log2(FoldChange)
-
-* SAINTscore v. Log2(FoldChange)
-
-- Filtered by SAINT Score
-
-* NSAF v. Log2(FoldChange)
-
-* SAINTscore v. Log2(FoldChange)  
-
-Output.txt
-- SAINTexpress "list.txt" output with additional columns that were used during the analysis
-  </help>
-</tool>