| Previous changeset 1:01f41cc043f3 (2015-11-19) Next changeset 3:e7d3a8865e8a (2015-11-19) |
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Commit message:
Deleted selected files |
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removed:
Bubblebeam_For_SAINT_wrapper.py Bubblebeam_For_SAINT_wrapper.xml |
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| diff -r 01f41cc043f3 -r efabd21af3ab Bubblebeam_For_SAINT_wrapper.py --- a/Bubblebeam_For_SAINT_wrapper.py Thu Nov 19 11:15:58 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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)) - |
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| diff -r 01f41cc043f3 -r efabd21af3ab Bubblebeam_For_SAINT_wrapper.xml --- a/Bubblebeam_For_SAINT_wrapper.xml Thu Nov 19 11:15:58 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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> |