| Next changeset 1:f70f75e89890 (2020-07-23) |
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flowcl/getOntology.R flowcl/getOntology.py flowcl/getOntology.xml flowcl/static/flowtools/css/flowCL.css flowcl/static/flowtools/js/flowcl_table.js flowcl/static/images/flowtools/flowcl_graph.png flowcl/static/images/flowtools/flowcl_summary.png flowcl/templates/flowCL.template flowcl/test-data/flowCL_res.pdf flowcl/test-data/flowCL_run_summary.txt flowcl/test-data/flowCL_table.txt flowcl/test-data/out.html |
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| diff -r 000000000000 -r fb0ee82f686d flowcl/getOntology.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flowcl/getOntology.R Mon Feb 27 12:56:34 2017 -0500 |
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| @@ -0,0 +1,28 @@ +# Cell Ontology Module for Galaxy +# FlowCL +###################################################################### +# Copyright (c) 2016 Northrop Grumman. +# All rights reserved. +###################################################################### +# +# Version 1 +# Cristel Thomas +# +# + +library(flowCL) +library(base) + +getOntology <- function(output_file, markers) { + res <- flowCL(markers, ResetArch = TRUE) + if (length(res) == 6) { + report <- capture.output(res$Table) + sink(output_file) + cat(report, sep = "\n") + sink() + } +} + +args <- commandArgs(trailingOnly = TRUE) +markers <- paste(args[3:length(args)], collapse="") +getOntology(args[2], markers) |
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| diff -r 000000000000 -r fb0ee82f686d flowcl/getOntology.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flowcl/getOntology.py Mon Feb 27 12:56:34 2017 -0500 |
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| @@ -0,0 +1,135 @@ +#!/usr/bin/env python +###################################################################### +# Copyright (c) 2016 Northrop Grumman. +# All rights reserved. +###################################################################### +from __future__ import print_function +import sys +import os + +from collections import defaultdict +from argparse import ArgumentParser +from jinja2 import Environment, FileSystemLoader + + +def generate_flowCL_query(list_markers, list_types): + if (len(list_markers) != len(list_types)): + return("pb with headers") + query = [] + # go through both lists, remove fsc/ssc + for i in range(0, len(list_markers)): + if not list_markers[i].startswith("FSC") and not list_markers[i].startswith("SSC"): + query.append(list_markers[i].upper()) + query.append(list_types[i]) + # return concatenated string + return("".join(query)) + + +def run_flowCL(phenotype, output_file, output_dir, tool_dir): + os.mkdir(output_dir) + tool = "/".join([tool_dir, "getOntology.R"]) + output_txt = "".join([output_dir, "/flowCL_run_summary.txt"]) + output_table = "".join([output_dir, "/flowCL_table.txt"]) + output_pdf = "".join([output_dir, "/flowCL_res.pdf"]) + run_command = " ". join(["Rscript --slave --vanilla", tool, "--args", output_txt, phenotype]) + os.system(run_command) + + table = defaultdict(list) + labels = [] + nb_match = 0 + if os.path.isfile(output_txt): + with open(output_txt, "r") as txt: + check = txt.readline().strip() + if (not check): + sys.exit(2) + else: + i = -1 + for lines in txt: + data = lines.strip("\n").split("\"") + if data[0].strip(): + labels.append(data[0].strip()) + i += 1 + if data[0].startswith("Score"): + count_matches = data[1].split(") ") + nb_match = len(count_matches) - 1 + table[i].append(data[1]) + else: + sys.stderr.write("There are no results with this query. Please check your markers if you believe there should be.") + sys.exit(2) + + with open(output_table, "w") as tbl: + tbl.write("1\t2\nQuery\t" + phenotype + "\n") + for j in table: + newline = " ".join(table[j]) + for k in range(1, nb_match + 1): + cur_stg = "".join([str(k+1), ")"]) + new_stg = "".join(["<br>", cur_stg]) + newline = newline.replace(cur_stg, new_stg) + + if labels[j] == "Cell ID": + cls = newline.split(" ") + for m in range(0, len(cls)): + if cls[m].startswith("CL"): + cl_id = cls[m].replace("_", ":") + link = "".join(['<a href="http://www.immport-labs.org/immport-ontology/public/home/home/', cl_id, '" target="_blank">']) + cls[m] = "".join([link, cls[m], "</a>"]) + newline = " ".join(cls) + tbl.write("\t".join([labels[j], newline]) + "\n") + + get_graph = " ".join(["mv flowCL_results/*.pdf", output_pdf]) + os.system(get_graph) + + env = Environment(loader=FileSystemLoader(tool_dir + "/templates")) + template = env.get_template("flowCL.template") + + real_directory = output_dir.replace("/job_working_directory", "") + context = {'outputDirectory': real_directory} + overview = template.render(**context) + with open(output_file, "w") as outf: + outf.write(overview) + return + + +if __name__ == "__main__": + parser = ArgumentParser( + prog="getOntology", + description="runs flowCL on a set of markers.") + + parser.add_argument( + '-m', + dest="markers", + required=True, + action='append', + help="marker queries.") + + parser.add_argument( + '-y', + dest="marker_types", + required=True, + action='append', + help="marker queries.") + + parser.add_argument( + '-o', + dest="output_file", + required=True, + help="Name of the output html file.") + + parser.add_argument( + '-d', + dest="output_dir", + required=True, + help="Path to the html supporting directory") + + parser.add_argument( + '-t', + dest="tool_dir", + required=True, + help="Path to the tool directory") + + args = parser.parse_args() + + markers = [m.strip() for m in args.markers] + query = generate_flowCL_query(markers, args.marker_types) + run_flowCL(query, args.output_file, args.output_dir, args.tool_dir) + sys.exit(0) |
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| diff -r 000000000000 -r fb0ee82f686d flowcl/getOntology.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flowcl/getOntology.xml Mon Feb 27 12:56:34 2017 -0500 |
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| @@ -0,0 +1,102 @@ +<tool id="get_cell_ontology" name="Explore cell ontology" version="1.0"> + <description>given a phenotype using flowCL.</description> + <requirements> + <requirement type="package" version="2.8">jinja2</requirement> + <requirement type="package" version="3.2.3">r</requirement> + <requirement type="package" version="1.11.1">bioconductor-flowcl</requirement> + </requirements> + <stdio> + <exit_code range="2" level="fatal" description="There was a problem running flowCL. You might want to check your marker names - See stderr for more details." /> + <exit_code range="3:" level="fatal" description="See stderr for more details." /> + </stdio> + <command><![CDATA[ + python $__tool_directory__/getOntology.py -o "${html_file}" -d "${html_file.files_path}" -t $__tool_directory__ -m "${marker1}" -y "${type1}" + #for $mrkrs in $Markers + -m "${mrkrs.markername}" + -y "${mrkrs.markertype}" + #end for + ]]> + </command> + <inputs> + <param name="marker1" type="text" label="First marker"/> + <param name="type1" type="select" label="First marker type"> + <option value="+">+</option> + <option value="-">-</option> + <option value="lo">lo</option> + <option value="lo">low</option> + <option value="lo">dim</option> + <option value="lo">--</option> + <option value="hi">hi</option> + <option value="hi">high</option> + <option value="hi">bri</option> + <option value="hi">bright</option> + <option value="hi">++</option> + </param> + <repeat name="Markers" title="Marker"> + <param name="markername" type="text" label="Add marker"/> + <param name="markertype" type="select" label="Marker type"> + <option value="+">+</option> + <option value="-">-</option> + <option value="lo">lo</option> + <option value="lo">low</option> + <option value="lo">dim</option> + <option value="lo">--</option> + <option value="hi">hi</option> + <option value="hi">high</option> + <option value="hi">bri</option> + <option value="hi">bright</option> + <option value="hi">++</option> + </param> + </repeat> + </inputs> + <outputs> + <data format="html" name="html_file" label="flowCL run"/> + </outputs> + <tests> + <test> + <param name="marker1" value="CD4"/> + <param name="type1" value="+"/> + <output name="html_file" file="out.html"> + <extra_files type="file" name="flowCL_res.pdf" value="flowCL_res.pdf" compare="contains"/> + <extra_files type="file" name="flowCL_run_summary.txt" value="flowCL_run_summary.txt"/> + <extra_files type="file" name="flowCL_table.txt" value="flowCL_table.txt"/> + </output> + </test> + </tests> + <help><![CDATA[ + This tool uses flowCL to find the most likely match to a given set a markers. + +----- + +**Input** + +Type in the marker names and select the expression level in the drop-down menu. + +**Output** + +A summary of the ouptut of flowCL is captured in a txt file. For more details, please refer to the flowCL documentation. + +**Graphical output** + +FlowCL generates a plot for the most likely matches to ontology. + +----- + +**Example** + +*Output summary* + +The CL terms hyperlink to their representation in the Immport Cell Ontology browser. + +.. image:: static/images/flowcl_summary.png + +*Graphical output* + +.. image:: static/flowtools/flowcl_graph.png + + ]]> + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btu807</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r fb0ee82f686d flowcl/static/flowtools/css/flowCL.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flowcl/static/flowtools/css/flowCL.css Mon Feb 27 12:56:34 2017 -0500 |
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| @@ -0,0 +1,43 @@ +/* +** DataTables config +*/ +div.dt-buttons { + float: right; +} + +th { + font-size:16px; + text-align: left; +} + +body td { + max-width: 50px; + font-size: 14px; + overflow: hidden; + text-overflow: ellipsis; +} + +.cltable thead { + display:none; +} + +.cltable td { + max-width: 40px; + word-break: break-all; + word-wrap: break-word; +} + +.firstcol { + width: 160px; +} + +.smallcols { + width: 100px; +} + +div.dataTables_wrapper { + width: 95%; + margin: 0 auto; +} + + |
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| diff -r 000000000000 -r fb0ee82f686d flowcl/static/flowtools/js/flowcl_table.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flowcl/static/flowtools/js/flowcl_table.js Mon Feb 27 12:56:34 2017 -0500 |
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| @@ -0,0 +1,28 @@ +// Copyright (c) 2016 Northrop Grumman. +// All rights reserved. + +var flowcl_table = './flowCL_table.txt'; + +var displayFlowCLTable = function(){ + d3.tsv(flowcl_table, function(error, data){ + if (error){ + alert("Problem retrieving data"); + return; + } + var fclHTML = '<table id="flowcltable" class="cltable display compact" cellspacing="0" width="100%"/>'; + $('#flowcl').html(fclHTML); + + var fclTableData = $.extend(true, [], data); + var fclTable = $('#flowcltable').DataTable({ + columns: [ + {"data":"1", className: 'firstcol'}, + {"data":"2"} + ], + dom: 't', + data: fclTableData, + buttons: [ + 'copy', 'pdfHtml5','csvHtml5' + ] + }); + }); +}; |
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| diff -r 000000000000 -r fb0ee82f686d flowcl/static/images/flowtools/flowcl_graph.png |
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| diff -r 000000000000 -r fb0ee82f686d flowcl/static/images/flowtools/flowcl_summary.png |
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| diff -r 000000000000 -r fb0ee82f686d flowcl/templates/flowCL.template --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flowcl/templates/flowCL.template Mon Feb 27 12:56:34 2017 -0500 |
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| @@ -0,0 +1,80 @@ +<!DOCTYPE html> +<html> +<head lang="en"> +<title>Flow CL Results</title> +<meta charset="UTF-8"> +<meta HTTP-EQUIV="Pragma" CONTENT="no-cache"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<link rel="stylesheet" href="/static/flowtools/bootstrap/css/bootstrap.css"/> +<link rel="stylesheet" href="/static/flowtools/select2/select2.min.css"/> +<link rel="stylesheet" href="/static/flowtools/css/flowCL.css"/> +<link rel="stylesheet" href="/static/flowtools/datatables/datatables.min.css"/> +<link rel="stylesheet" href="/static/flowtools/datatables/Buttons-1.1.2/css/buttons.dataTables.min.css"/> +<link rel="stylesheet" href="/static/flowtools/datatables/Select-1.1.2/css/select.dataTables.min.css"/> +<script src="/static/flowtools/jquery-1.11.3.min.js" type="text/javascript"></script> +<script src="/static/flowtools/bootstrap/js/bootstrap.js" type="text/javascript"></script> +<script src="/static/flowtools/select2/select2.full.min.js" type="text/javascript"></script> +<script src="/static/flowtools/d3/d3.min.js" type="text/javascript"></script> +<script src="/static/flowtools/datatables/datatables.min.js" type="text/javascript"></script> +<script src="/static/flowtools/js/flowcl_table.js" type="text/javascript"></script> + +<style> +#input{font-family:Calibri,Arial} +table.dataTable tbody td.dt-body-right { + text-align: right; +} +#div{padding:5px;width:150px;height:100px;text-align:center} +table{width:100%;border:0px solid;border-collapse:collapse;text-align:left;} +th{background-color:#3e6db0;color:#fff;padding:5px} +</style> +</head> + +<body> +<div class="container-fluid"> + <div class="row" style="padding-bottom:10px;min-height:500px;"> + <div class="col-md-12"> + <ul class="nav nav-tabs tabs-main"> + <li class="homeTab active" data-value="flowcl"><a href="#flowcl" data-toggle="tab">FlowCL Results Summary</a></li> + <li class="homeTab" data-value="graph"><a href="#graph" data-toggle="tab">Graphical Representation</a></li> + </ul> + + <div class="tab-content"> + <div class="tab-pane active" id="flowcl" style="min-height:500px;"> + <div class="row"> + <div id="flowcl"/> + </div> + </div> + </div> + <div class="tab-pane" id="graph" style="height:800px;"> + <embed src="./flowCL_res.pdf" width="100%" height="100%" alt="pdf" pluginspage="http://www.adobe.com/products/acrobat/readstep2.html"> + </div> + </div> + </div> +</div> + + +</div> +</div> + + +<script> +var summaryLoaded = false; + +$().ready(function() { + $(document).on('shown.bs.tab','a[data-toggle="tab"]', function(e) { + var tab = e.target.getAttribute("href"); + if (tab == '#flowcl') { + if (summaryLoaded) { + return true; + } + summaryLoaded = true; + displayFlowCLTable(); + } + }); + + summaryLoaded = true; + displayFlowCLTable(); +}); +</script> +</body> +</html> |
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| diff -r 000000000000 -r fb0ee82f686d flowcl/test-data/flowCL_res.pdf |
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| diff -r 000000000000 -r fb0ee82f686d flowcl/test-data/flowCL_run_summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flowcl/test-data/flowCL_run_summary.txt Mon Feb 27 12:56:34 2017 -0500 |
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| @@ -0,0 +1,24 @@ + [,1] +Short marker names "CD4+" +Ontology marker names "CD4 molecule" +Experiment markers "CD4" +Ontology exper. names "CD4 molecule" +Successful Match? "No" +Marker ID "1) PR_000001004 2) PR_000001004 3) PR_000001004 4) PR_000001004 5)" + "PR_000001004 + more" +Marker Label "1) CD4 molecule 2) CD4 molecule 3) CD4 molecule 4) CD4 molecule 5)" + "CD4 molecule + more" +Marker Key "1) { } CD4+ ( ) [ alpha-beta T cell receptor complex+, T cell" + "receptor co-receptor CD8+ ] 2) { } CD4+ ( ) [ alpha-beta T cell" + "receptor complex+, T cell receptor co-receptor CD8+ ] 3) { } CD4+ ( )" + "[ alpha-beta T cell receptor complex+, T cell receptor co-receptor" + "CD8+ ] 4) { } CD4+ ( ) [ T-cell surface glycoprotein CD8 alpha" + "chain-, alpha-beta T cell receptor complex+ ] 5) { } CD4+ ( ) [ T" + "cell receptor co-receptor CD8-, alpha-beta T cell receptor complex+," + "CD3+ ] + more" +Score (Out of 1) "1) 0.333 2) 0.333 3) 0.333 4) 0.333 5) 0.25 + more" +Cell ID "1) CL_0000809 2) CL_0002427 3) CL_0002428 4) CL_0000810 5) CL_0000492" + "+ more" +Cell Label "1) double-positive, alpha-beta thymocyte 2) resting double-positive" + "thymocyte 3) double-positive blast 4) CD4-positive, alpha-beta" + "thymocyte 5) CD4-positive helper T cell + more" |
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| diff -r 000000000000 -r fb0ee82f686d flowcl/test-data/flowCL_table.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flowcl/test-data/flowCL_table.txt Mon Feb 27 12:56:34 2017 -0500 |
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| @@ -0,0 +1,12 @@ +1 2 +Short marker names CD4+ +Ontology marker names CD4 molecule +Experiment markers CD4 +Ontology exper. names CD4 molecule +Successful Match? No +Marker ID 1) PR_000001004 <br>2) PR_000001004 <br>3) PR_000001004 <br>4) PR_000001004 <br>5) PR_000001004 + more +Marker Label 1) CD4 molecule <br>2) CD4 molecule <br>3) CD4 molecule <br>4) CD4 molecule <br>5) CD4 molecule + more +Marker Key 1) { } CD4+ ( ) [ alpha-beta T cell receptor complex+, T cell receptor co-receptor CD8+ ] <br>2) { } CD4+ ( ) [ alpha-beta T cell receptor complex+, T cell receptor co-receptor CD8+ ] <br>3) { } CD4+ ( ) [ alpha-beta T cell receptor complex+, T cell receptor co-receptor CD8+ ] <br>4) { } CD4+ ( ) [ T-cell surface glycoprotein CD8 alpha chain-, alpha-beta T cell receptor complex+ ] <br>5) { } CD4+ ( ) [ T cell receptor co-receptor CD8-, alpha-beta T cell receptor complex+, CD3+ ] + more +Score (Out of 1) 1) 0.333 <br>2) 0.333 <br>3) 0.333 <br>4) 0.333 <br>5) 0.25 + more +Cell ID 1) <a href="http://www.immport-labs.org/immport-ontology/public/home/home/CL:0000809" target="_blank">CL_0000809</a> <br>2) <a href="http://www.immport-labs.org/immport-ontology/public/home/home/CL:0002427" target="_blank">CL_0002427</a> <br>3) <a href="http://www.immport-labs.org/immport-ontology/public/home/home/CL:0002428" target="_blank">CL_0002428</a> <br>4) <a href="http://www.immport-labs.org/immport-ontology/public/home/home/CL:0000810" target="_blank">CL_0000810</a> <br>5) <a href="http://www.immport-labs.org/immport-ontology/public/home/home/CL:0000492" target="_blank">CL_0000492</a> + more +Cell Label 1) double-positive, alpha-beta thymocyte <br>2) resting double-positive thymocyte <br>3) double-positive blast <br>4) CD4-positive, alpha-beta thymocyte <br>5) CD4-positive helper T cell + more |
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| diff -r 000000000000 -r fb0ee82f686d flowcl/test-data/out.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flowcl/test-data/out.html Mon Feb 27 12:56:34 2017 -0500 |
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| @@ -0,0 +1,80 @@ +<!DOCTYPE html> +<html> +<head lang="en"> +<title>Flow CL Results</title> +<meta charset="UTF-8"> +<meta HTTP-EQUIV="Pragma" CONTENT="no-cache"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<link rel="stylesheet" href="/static/flowtools/bootstrap/css/bootstrap.css"/> +<link rel="stylesheet" href="/static/flowtools/select2/select2.min.css"/> +<link rel="stylesheet" href="/static/flowtools/css/flowCL.css"/> +<link rel="stylesheet" href="/static/flowtools/datatables/datatables.min.css"/> +<link rel="stylesheet" href="/static/flowtools/datatables/Buttons-1.1.2/css/buttons.dataTables.min.css"/> +<link rel="stylesheet" href="/static/flowtools/datatables/Select-1.1.2/css/select.dataTables.min.css"/> +<script src="/static/flowtools/jquery-1.11.3.min.js" type="text/javascript"></script> +<script src="/static/flowtools/bootstrap/js/bootstrap.js" type="text/javascript"></script> +<script src="/static/flowtools/select2/select2.full.min.js" type="text/javascript"></script> +<script src="/static/flowtools/d3/d3.min.js" type="text/javascript"></script> +<script src="/static/flowtools/datatables/datatables.min.js" type="text/javascript"></script> +<script src="/static/flowtools/js/flowcl_table.js" type="text/javascript"></script> + +<style> +#input{font-family:Calibri,Arial} +table.dataTable tbody td.dt-body-right { + text-align: right; +} +#div{padding:5px;width:150px;height:100px;text-align:center} +table{width:100%;border:0px solid;border-collapse:collapse;text-align:left;} +th{background-color:#3e6db0;color:#fff;padding:5px} +</style> +</head> + +<body> +<div class="container-fluid"> + <div class="row" style="padding-bottom:10px;min-height:500px;"> + <div class="col-md-12"> + <ul class="nav nav-tabs tabs-main"> + <li class="homeTab active" data-value="flowcl"><a href="#flowcl" data-toggle="tab">FlowCL Results Summary</a></li> + <li class="homeTab" data-value="graph"><a href="#graph" data-toggle="tab">Graphical Representation</a></li> + </ul> + + <div class="tab-content"> + <div class="tab-pane active" id="flowcl" style="min-height:500px;"> + <div class="row"> + <div id="flowcl"/> + </div> + </div> + </div> + <div class="tab-pane" id="graph" style="height:800px;"> + <embed src="./flowCL_res.pdf" width="100%" height="100%" alt="pdf" pluginspage="http://www.adobe.com/products/acrobat/readstep2.html"> + </div> + </div> + </div> +</div> + + +</div> +</div> + + +<script> +var summaryLoaded = false; + +$().ready(function() { + $(document).on('shown.bs.tab','a[data-toggle="tab"]', function(e) { + var tab = e.target.getAttribute("href"); + if (tab == '#flowcl') { + if (summaryLoaded) { + return true; + } + summaryLoaded = true; + displayFlowCLTable(); + } + }); + + summaryLoaded = true; + displayFlowCLTable(); +}); +</script> +</body> +</html> \ No newline at end of file |
