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Bubblebeam_For_SAINT_wrapper.xml |
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| diff -r cb7223752458 -r 64b822045467 Bubblebeam_For_SAINT_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Bubblebeam_For_SAINT_wrapper.xml Fri Jan 29 09:33:45 2016 -0500 |
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| @@ -0,0 +1,146 @@ +<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|error" + source="stdout" + level="fatal" + description="Unknown error"/> + <regex match="Error|error" + source="stderr" + level="fatal" + description="Unknown error"/> + <regex match="Error: bad bait" + source="stdout" + level="fatal" + description="Error: bad bait"/> + </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: + +MaxQuant or Scaffold: + +Select Scaffold if using Scaffold output and MaxQunat if using pepetides.txt from MaxQuant software. + +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 + +List of Uniprot IDs to Include: + +Text file with one column of uniprot IDs. Only the Uniprot IDs in the file will be used on the resulting bubblebeam. + +List of Uniprot IDs to Exclude: + +Text file with one column of uniprot IDs. The Uniprot IDs in this list will not be used in generating the bubblebeam. + +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> |