# HG changeset patch
# User azomics
# Date 1595508618 14400
# Node ID f70f75e89890e429b5d1795126abc59bf13c6998
# Parent fb0ee82f686d2e72736169ea1541f17e87056a4b
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowcl commit d59d95d2bc6a64eb5c37b8291a7c314754c2067f"
diff -r fb0ee82f686d -r f70f75e89890 flowcl/getOntology.R
--- a/flowcl/getOntology.R Mon Feb 27 12:56:34 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-# 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)
diff -r fb0ee82f686d -r f70f75e89890 flowcl/getOntology.py
--- a/flowcl/getOntology.py Mon Feb 27 12:56:34 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,135 +0,0 @@
-#!/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(["
", 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([''])
- cls[m] = "".join([link, cls[m], ""])
- 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)
diff -r fb0ee82f686d -r f70f75e89890 flowcl/getOntology.xml
--- a/flowcl/getOntology.xml Mon Feb 27 12:56:34 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,102 +0,0 @@
-
- given a phenotype using flowCL.
-
- jinja2
- r
- bioconductor-flowcl
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- 10.1093/bioinformatics/btu807
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diff -r fb0ee82f686d -r f70f75e89890 flowcl/static/flowtools/css/flowCL.css
--- a/flowcl/static/flowtools/css/flowCL.css Mon Feb 27 12:56:34 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-/*
-** 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;
-}
-
-
diff -r fb0ee82f686d -r f70f75e89890 flowcl/static/flowtools/js/flowcl_table.js
--- a/flowcl/static/flowtools/js/flowcl_table.js Mon Feb 27 12:56:34 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-// 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 = '';
- $('#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'
- ]
- });
- });
-};
diff -r fb0ee82f686d -r f70f75e89890 flowcl/static/images/flowtools/flowcl_graph.png
Binary file flowcl/static/images/flowtools/flowcl_graph.png has changed
diff -r fb0ee82f686d -r f70f75e89890 flowcl/static/images/flowtools/flowcl_summary.png
Binary file flowcl/static/images/flowtools/flowcl_summary.png has changed
diff -r fb0ee82f686d -r f70f75e89890 flowcl/templates/flowCL.template
--- a/flowcl/templates/flowCL.template Mon Feb 27 12:56:34 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,80 +0,0 @@
-
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-Flow CL Results
-
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diff -r fb0ee82f686d -r f70f75e89890 flowcl/test-data/flowCL_res.pdf
Binary file flowcl/test-data/flowCL_res.pdf has changed
diff -r fb0ee82f686d -r f70f75e89890 flowcl/test-data/flowCL_run_summary.txt
--- a/flowcl/test-data/flowCL_run_summary.txt Mon Feb 27 12:56:34 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
- [,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"
diff -r fb0ee82f686d -r f70f75e89890 flowcl/test-data/flowCL_table.txt
--- a/flowcl/test-data/flowCL_table.txt Mon Feb 27 12:56:34 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-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
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
diff -r fb0ee82f686d -r f70f75e89890 flowcl/test-data/out.html
--- a/flowcl/test-data/out.html Mon Feb 27 12:56:34 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,80 +0,0 @@
-
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-Flow CL Results
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diff -r fb0ee82f686d -r f70f75e89890 getOntology.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/getOntology.R Thu Jul 23 08:50:18 2020 -0400
@@ -0,0 +1,29 @@
+#!/usr/bin/Rscript --vanilla
+# Cell Ontology Module for Galaxy
+# FlowCL
+######################################################################
+# Copyright (c) 2016 Northrop Grumman.
+# All rights reserved.
+######################################################################
+#
+# Version 1
+# Cristel Thomas
+#
+#
+
+suppressWarnings(suppressMessages(library(flowCL)))
+suppressWarnings(suppressMessages(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[2:length(args)], collapse="")
+getOntology(args[1], markers)
diff -r fb0ee82f686d -r f70f75e89890 getOntology.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/getOntology.py Thu Jul 23 08:50:18 2020 -0400
@@ -0,0 +1,134 @@
+#!/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, 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(["
", 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([''])
+ cls[m] = "".join([link, cls[m], ""])
+ 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)
diff -r fb0ee82f686d -r f70f75e89890 getOntology.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/getOntology.xml Thu Jul 23 08:50:18 2020 -0400
@@ -0,0 +1,102 @@
+
+ given a phenotype using flowCL
+
+ jinja2
+ bioconductor-flowcl
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diff -r fb0ee82f686d -r f70f75e89890 static/images/flowtools/flowcl_graph.png
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diff -r fb0ee82f686d -r f70f75e89890 static/images/flowtools/flowcl_summary.png
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diff -r fb0ee82f686d -r f70f75e89890 templates/flowCL.template
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/flowCL.template Thu Jul 23 08:50:18 2020 -0400
@@ -0,0 +1,79 @@
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diff -r fb0ee82f686d -r f70f75e89890 test-data/flowCL_res.pdf
Binary file test-data/flowCL_res.pdf has changed
diff -r fb0ee82f686d -r f70f75e89890 test-data/flowCL_run_summary.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flowCL_run_summary.txt Thu Jul 23 08:50:18 2020 -0400
@@ -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"
diff -r fb0ee82f686d -r f70f75e89890 test-data/flowCL_table.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/flowCL_table.txt Thu Jul 23 08:50:18 2020 -0400
@@ -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
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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