# HG changeset patch
# User galaxyp
# Date 1623521153 0
# Node ID adb808a154098719e99385dd3b812de21faffd0f
"planemo upload commit 47d779aa1de5153673ac8bb1e37c9730210cbb5d"
diff -r 000000000000 -r adb808a15409 README.rst
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+Wrapper for JVenn Diagram Tool
+==============================
+
+**Authors**
+
+Philippe Bardou, Jérôme Mariette, Frédéric Escudié, Christophe Djemiel and Christophe Klopp. jvenn: an interactive Venn diagram viewer. BMC Bioinformatics 2014, 15:293 doi:10.1186/1471-2105-15-293
+
+**Galaxy integration**
+
+T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+
+Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform
+
+Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
+
+------------------------------
+
+This tool draw a venn diagram from lists/files using Jvenn plug-in (http://jvenn.toulouse.inra.fr/app/index.html). It also creates output files that contain common or specific elements between query and each compared lists/files.
+
+**Inputs**
+
+* **Query file:** A file containing different information of proteins, could be output of previous components.
+
+* **File of a list of IDs:** .TXT format, each line contains 1 ID
+
+ AMY1A
+
+ ALB
+
+ IGKC
+
+ CSTA
+
+ IGHA1
+
+ ACTG1
+
+* **List of IDs:** IDs separated by a space
+ AMY1A ALB IGKC CSTA IGHA1 ACTG1
+
+If you choose a file, it is necessary to specify the column where you would like to perform the comparison.
+
+**Outputs**
+
+* **Summary file** (venn_diagram_summary.html):
+ Venn diagram: Could be downloaded as image (PNG, SVG)
+
+* **Venn text output file**
+ A text file containing common/specific elements among compared lists/files.
diff -r 000000000000 -r adb808a15409 jvenn_template.html
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+ Jvenn+
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+ javascript is needed to display data.
+ If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.
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+ javascript is needed to display data.
+ If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.
+
+ javascript is needed to display data.
+ If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.
+
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diff -r 000000000000 -r adb808a15409 venn_diagram.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/venn_diagram.py Sat Jun 12 18:05:53 2021 +0000
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+#!/usr/bin/env python
+
+import argparse
+import csv
+import json
+import os
+import re
+from itertools import combinations
+
+
+CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
+
+########################################################################
+# FUNCTIONS
+########################################################################
+
+
+def isnumber(format, n):
+ """
+ Check if an element is integer or float
+ """
+ float_format = re.compile(r"^[-]?[1-9][0-9]*.?[0-9]+$")
+ int_format = re.compile(r"^[-]?[1-9][0-9]*$")
+ test = ""
+ if format == "int":
+ test = re.match(int_format, n)
+ elif format == "float":
+ test = re.match(float_format, n)
+ if test:
+ return True
+ else:
+ return False
+
+
+def input_to_dict(inputs):
+ """
+ Parse input and return a dictionary of name and data of each lists/files
+ """
+ comp_dict = {}
+ title_dict = {}
+ c = ["A", "B", "C", "D", "E", "F"]
+ for i in range(len(inputs)):
+ input_file = inputs[i][0]
+ name = inputs[i][1]
+ input_type = inputs[i][2]
+ title = c[i]
+ title_dict[title] = name
+ ids = set()
+ if input_type == "file":
+ header = inputs[i][3]
+ ncol = inputs[i][4]
+ with open(input_file, "r") as handle:
+ file_content = csv.reader(handle, delimiter="\t")
+ file_content = list(file_content) # csv object to list
+
+ # Check if column number is in right form
+ if isnumber("int", ncol.replace("c", "")):
+ if header == "true":
+ # gets ids from defined column
+ file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content[1:]]] # noqa 501
+
+ else:
+ file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content]] # noqa 501
+ else:
+ raise ValueError("Please fill in the right format of column number") # noqa 501
+ else:
+ ids = set()
+ file_content = inputs[i][0].split()
+ file_content = [x.split(";") for x in file_content]
+
+ # flat list of list of lists, remove empty items
+ file_content = [item.strip() for sublist in file_content for item in sublist if item != ''] # noqa 501
+ ids.update(file_content)
+ if 'NA' in ids:
+ ids.remove('NA')
+ comp_dict[title] = ids
+
+ return comp_dict, title_dict
+
+
+def intersect(comp_dict):
+ """
+ Calculate the intersections of input
+ """
+ names = set(comp_dict)
+ for i in range(1, len(comp_dict) + 1):
+ for group in combinations(sorted(comp_dict), i):
+ others = set()
+ [others.add(name) for name in names if name not in group]
+ difference = []
+ intersected = set.intersection(*(comp_dict[k] for k in group))
+ if len(others) > 0:
+ difference = intersected.difference(set.union(*(comp_dict[k] for k in others))) # noqa 501
+ yield group, list(intersected), list(difference)
+
+
+def diagram(comp_dict, title_dict):
+ """
+ Create json string for jvenn diagram plot
+ """
+ result = {}
+ result["name"] = {}
+ for k in comp_dict.keys():
+ result["name"][k] = title_dict[k]
+
+ result["data"] = {}
+ result["values"] = {}
+ for group, intersected, difference in intersect(comp_dict):
+ if len(group) == 1:
+ result["data"]["".join(group)] = sorted(difference)
+ result["values"]["".join(group)] = len(difference)
+ elif len(group) > 1 and len(group) < len(comp_dict):
+ result["data"]["".join(group)] = sorted(difference)
+ result["values"]["".join(group)] = len(difference)
+ elif len(group) == len(comp_dict):
+ result["data"]["".join(group)] = sorted(intersected)
+ result["values"]["".join(group)] = len(intersected)
+
+ return result
+
+# Write intersections of input to text output file
+
+
+def write_text_venn(json_result):
+ lines = []
+ result = dict((k, v) for k, v in json_result["data"].items() if v != []) # noqa 501
+ for key in result:
+ if 'NA' in result[key]:
+ result[key].remove("NA")
+
+ list_names = dict((k, v) for k, v in json_result["name"].items() if v != []) # noqa 501
+ nb_lines_max = max(len(v) for v in result.values())
+
+ # get list names associated to each column
+ column_dict = {}
+ for key in result:
+ if key in list_names:
+ column_dict[key] = list_names[key]
+ else:
+ keys = list(key)
+ column_dict[key] = "_".join([list_names[k] for k in keys])
+
+ # construct tsv
+ for key in result:
+ line = result[key]
+ if len(line) < nb_lines_max:
+ line.extend([''] * (nb_lines_max - len(line)))
+ line = [column_dict[key]] + line # add header
+ lines.append(line)
+ # transpose tsv
+ lines = zip(*lines)
+
+ with open("venn_diagram_text_output.tsv", "w") as output:
+ tsv_output = csv.writer(output, delimiter='\t')
+ tsv_output.writerows(lines)
+
+
+def write_summary(summary_file, inputs):
+ """
+ Paste json string into template file
+ """
+ a, b = input_to_dict(inputs)
+ data = diagram(a, b)
+ write_text_venn(data)
+
+ to_replace = {
+ "series": [data],
+ "displayStat": "true",
+ "displaySwitch": "true",
+ "shortNumber": "true",
+ }
+
+ FH_summary_tpl = open(os.path.join(CURRENT_DIR, "jvenn_template.html"))
+ FH_summary_out = open(summary_file, "w")
+ for line in FH_summary_tpl:
+ if "###JVENN_DATA###" in line:
+ line = line.replace("###JVENN_DATA###", json.dumps(to_replace))
+ FH_summary_out.write(line)
+
+ FH_summary_out.close()
+ FH_summary_tpl.close()
+
+
+def process(args):
+ write_summary(args.summary, args.input)
+
+
+#####################################################################
+# MAIN
+#####################################################################
+if __name__ == '__main__':
+ # Parse parameters
+ parser = argparse.ArgumentParser(description='Filters an abundance file')
+ group_input = parser.add_argument_group('Inputs')
+ group_input.add_argument('--input', nargs="+", action="append",
+ required=True, help="The input tabular file.")
+ group_output = parser.add_argument_group('Outputs')
+ group_output.add_argument('--summary', default="summary.html",
+ help="The HTML file containing the graphs. \
+ [Default: %(default)s]")
+ args = parser.parse_args()
+
+ # Process
+ process(args)
diff -r 000000000000 -r adb808a15409 venn_diagram.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/venn_diagram.xml Sat Jun 12 18:05:53 2021 +0000
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+ with JVenn
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+ python
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+ doi:10.1186/1471-2105-15-293
+ @book{toolsProteoRE,
+ journal = {GitHub repository},
+ publisher = {GitHub},
+ title = {ProteoRE tools},
+ url = {https://github.com/galaxyproteomics/tools-galaxyp},
+ author = {Lien Nguyen, David Chistiany, Florence Combes,Christophe Caron, Valentin Loux Yves Vandenbrouck},
+ date = {2021},
+ year = {2021},
+ }
+
+