# HG changeset patch
# User tomnl
# Date 1485961397 18000
# Node ID 8f5496765a2213cfd3b1d39ddc694879741c262d
Uploaded
diff -r 000000000000 -r 8f5496765a22 mzml2isa-galaxy-master/.gitignore
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mzml2isa-galaxy-master/.gitignore Wed Feb 01 10:03:17 2017 -0500
@@ -0,0 +1,6 @@
+*.pyc
+.idea
+*.egg-info
+.egg
+*~
+
diff -r 000000000000 -r 8f5496765a22 mzml2isa-galaxy-master/.travis.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mzml2isa-galaxy-master/.travis.yml Wed Feb 01 10:03:17 2017 -0500
@@ -0,0 +1,16 @@
+language: python
+
+before_install:
+ - sudo apt-get install -y python-virtualenv
+ - virtualenv planemo-venv
+ - . planemo-venv/bin/activate
+ - pip install --upgrade pip setuptools
+ - pip install planemo
+ - planemo conda_init
+
+install:
+ - planemo conda_install ${TRAVIS_BUILD_DIR}/galaxy/mzml2isa/
+
+script:
+ - planemo test --install_galaxy --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR}/galaxy/mzml2isa/ --galaxy_branch "dev"
+
diff -r 000000000000 -r 8f5496765a22 mzml2isa-galaxy-master/README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mzml2isa-galaxy-master/README.md Wed Feb 01 10:03:17 2017 -0500
@@ -0,0 +1,5 @@
+mzml2isa for galaxy
+===============
+
+[](http://bioconda.github.io/recipes/mzml2isa/README.html) [](https://travis-ci.org/ISA-tools/mzml2isa-galaxy)
+
diff -r 000000000000 -r 8f5496765a22 mzml2isa-galaxy-master/galaxy/mzml2isa/README.rst
diff -r 000000000000 -r 8f5496765a22 mzml2isa-galaxy-master/galaxy/mzml2isa/mzml2isa.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mzml2isa-galaxy-master/galaxy/mzml2isa/mzml2isa.xml Wed Feb 01 10:03:17 2017 -0500
@@ -0,0 +1,258 @@
+
+ Parser to get meta information from mzML files and create an ISA-Tab structure
+
+
+ mzml2isa_macros.xml
+
+
+
i_Investigation.txt
s_test.txt
diff -r 000000000000 -r 8f5496765a22 mzml2isa-galaxy-master/galaxy/mzml2isa/test-data/metabolomics_study/test/s_test.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mzml2isa-galaxy-master/galaxy/mzml2isa/test-data/metabolomics_study/test/s_test.txt Wed Feb 01 10:03:17 2017 -0500
@@ -0,0 +1,7 @@
+"Source Name" "Characteristics[Organism]" "Term Source REF" "Term Accession Number" "Characteristics[Variant]" "Term Source REF" "Term Accession Number" "Characteristics[Organism part]" "Term Source REF" "Term Accession Number" "Protocol REF" "Sample Name"
+"" "" "" "" "" "" "" "" "" "" "Sample collection" "5_samp"
+"" "" "" "" "" "" "" "" "" "" "Sample collection" "3_samp"
+"" "" "" "" "" "" "" "" "" "" "Sample collection" "2_samp"
+"" "" "" "" "" "" "" "" "" "" "Sample collection" "1_samp"
+"" "" "" "" "" "" "" "" "" "" "Sample collection" "6_samp"
+"" "" "" "" "" "" "" "" "" "" "Sample collection" "4_samp"
diff -r 000000000000 -r 8f5496765a22 mzml2isa-galaxy-master/galaxy/mzml2isa/tool-data/get_status_ont.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mzml2isa-galaxy-master/galaxy/mzml2isa/tool-data/get_status_ont.py Wed Feb 01 10:03:17 2017 -0500
@@ -0,0 +1,51 @@
+import sys
+import os
+import json
+import urllib.error
+import urllib.request as rq
+from urllib.parse import quote
+import csv
+
+###############################################################################
+# Python3 script to get tab seperated maf_index.loc files for drop down menus
+###############################################################################
+# Code modified from mzm2isa-qt python package developed by Martin Larralde
+# https://github.com/althonos/mzml2isa-qt/scrapers.py
+
+
+def get_ont_loc(jsonSourceUrl, sparName, ontoClass, filepth):
+ onto = json.loads(rq.urlopen(jsonSourceUrl).read().decode('utf-8'))
+ info = []
+ for x in onto:
+ if '@type' in x:
+ if ontoClass in x['@type']:
+ info.append(x)
+ info = [ (x['http://www.w3.org/2000/01/rdf-schema#label'],x['@id']) for x in info ]
+
+ ontd = {x[0]['@value'].capitalize():y for (x,y) in info}
+
+ with open(filepth, 'w') as f:
+ writer = csv.writer(f, delimiter='\t', quoting=csv.QUOTE_ALL)
+ writer.writerow(["name", "link"])
+ for key, value in ontd.items():
+ writer.writerow([key, value])
+
+ return ontd
+
+#-------------------------------
+# publication status ontology
+#-------------------------------
+jsonSourceUrl = "http://www.sparontologies.net/ontologies/pso/source.json"
+sparName = "pso"
+ontoClass = "http://purl.org/spar/pso/PublicationStatus"
+get_ont_loc(jsonSourceUrl, sparName, ontoClass, './pub_status.loc')
+
+#-------------------------------
+# Job role ontology
+#-------------------------------
+jsonSourceUrl = "http://www.sparontologies.net/ontologies/pro/source.json"
+sparName = "pro"
+ontoClass = "http://purl.org/spar/pro/PublishingRole"
+get_ont_loc(jsonSourceUrl, sparName, ontoClass, './pub_role.loc')
+
+
diff -r 000000000000 -r 8f5496765a22 mzml2isa-galaxy-master/galaxy/mzml2isa/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mzml2isa-galaxy-master/galaxy/mzml2isa/tool_dependencies.xml Wed Feb 01 10:03:17 2017 -0500
@@ -0,0 +1,7 @@
+
+
+
+
+
+
+
diff -r 000000000000 -r 8f5496765a22 mzml2isa-galaxy-master/galaxy/mzml2isa/wrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mzml2isa-galaxy-master/galaxy/mzml2isa/wrapper.py Wed Feb 01 10:03:17 2017 -0500
@@ -0,0 +1,238 @@
+#!/usr/bin/env python
+
+import sys
+import json
+import os
+import argparse
+import textwrap
+import csv
+import inspect
+
+
+def ontology_lookup(name, table):
+ # takes in accession number outputs the name
+ filename = inspect.getframeinfo(inspect.currentframe()).filename
+ path = os.path.dirname(os.path.abspath(filename))
+
+
+ # check if correct table
+ if table=="role":
+ tablepth = os.path.join(path, 'pub_role.loc')
+ elif table=="status":
+ tablepth = os.path.join(path, 'pub_status.loc')
+ else:
+ print "Table not recognised"
+ return ""
+
+ with open(tablepth, "rb") as csvfile:
+ reader = csv.reader(csvfile, delimiter='\t')
+ ont_dict = dict((k, v) for v, k in reader)
+ try:
+ return ont_dict[name]
+ except KeyError:
+ return ""
+
+
+
+def main():
+
+ p = argparse.ArgumentParser(prog='PROG',
+ formatter_class=argparse.RawDescriptionHelpFormatter,
+ description='''DI-MS processing for DMA''',
+ epilog=textwrap.dedent('''\
+ -------------------------------------------------------------------------
+ '''))
+
+
+ p.add_argument('-inputzip', dest='inputzip', required=True)
+ p.add_argument('-out_dir', dest='out_dir', required=True)
+ p.add_argument('-html_file', dest='html_file', required=True)
+ p.add_argument('-study_title', dest='study_title', required=True)
+
+ p.add_argument('-jsontxt', dest='jsontxt', required=False, nargs='?')
+
+ p.add_argument('--s_submission_date', dest='s_submission_date', required=False, default="", nargs='?')
+ p.add_argument('--s_release_date', dest='s_release_date', required=False, default="", nargs='?')
+ p.add_argument('--s_description', dest='s_description', required=False, default="", nargs='?')
+ p.add_argument('--s_pubmed', dest='s_pubmed', required=False, default="", nargs='?')
+ p.add_argument('--s_pub_doi', dest='s_pub_doi', required=False, default="", nargs='?')
+ p.add_argument('--s_pub_status', dest='s_pub_status', required=False, default="", nargs='?')
+ p.add_argument('--s_pub_author', dest='s_pub_author', required=False, default="", nargs='?')
+ p.add_argument('--s_pub_title', dest='s_pub_title', required=False, default="", nargs='?')
+ p.add_argument('--s_first_name', dest='s_first_name', required=False, default="", nargs='?')
+ p.add_argument('--s_mid_initials', dest='s_mid_initials', required=False, default="", nargs='?')
+ p.add_argument('--s_last_name', dest='s_last_name', required=False, default="", nargs='?')
+ p.add_argument('--s_telephone', dest='s_telephone', required=False, default="", nargs='?')
+ p.add_argument('--s_fax', dest='s_fax', required=False, default="", nargs='?')
+ p.add_argument('--s_affiliation', dest='s_affiliation', required=False, default="", nargs='?')
+ p.add_argument('--s_role', dest='s_role', required=False, default="", nargs='?')
+ p.add_argument('--s_mail', dest='s_mail', required=False, default="", nargs='?')
+ p.add_argument('--s_address', dest='s_address', required=False, default="", nargs='?')
+ p.add_argument('--i_submission_date', dest='i_submission_date', required=False, default="", nargs='?')
+ p.add_argument('--i_release_date', dest='i_release_date', required=False, default="", nargs='?')
+ p.add_argument('--i_description', dest='i_description', required=False, default="", nargs='?')
+ p.add_argument('--i_pubmed', dest='i_pubmed', required=False, default="", nargs='?')
+ p.add_argument('--i_pub_doi', dest='i_pub_doi', required=False, default="", nargs='?')
+ p.add_argument('--i_pub_title', dest='i_pub_title', required=False, default="", nargs='?')
+ p.add_argument('--i_pub_status', dest='i_pub_status', required=False, default="", nargs='?')
+ p.add_argument('--i_pub_author', dest='i_pub_author', required=False, default="", nargs='?')
+ p.add_argument('--i_first_name', dest='i_first_name', required=False, default="", nargs='?')
+ p.add_argument('--i_mid_initials', dest='i_mid_initials', required=False, default="", nargs='?')
+ p.add_argument('--i_last_name', dest='i_last_name', required=False, default="", nargs='?')
+ p.add_argument('--i_telephone', dest='i_telephone', required=False, default="", nargs='?')
+ p.add_argument('--i_fax', dest='i_fax', required=False, default="", nargs='?')
+ p.add_argument('--i_affiliation', dest='i_affiliation', required=False, default="", nargs='?')
+ p.add_argument('--i_role', dest='i_role', required=False, default="", nargs='?')
+ p.add_argument('--i_mail', dest='i_mail', required=False, default="", nargs='?')
+ p.add_argument('--i_address', dest='i_address', required=False, default="", nargs='?')
+ p.add_argument('--organism_text', dest='organism_text', required=False, default="", nargs='?')
+ p.add_argument('--organism_ref', dest='organism_ref', required=False, default="", nargs='?')
+ p.add_argument('--organism_iri', dest='organism_iri', required=False, default="", nargs='?')
+ p.add_argument('--organism_part_text', dest='organism_part_text', required=False, default="", nargs='?')
+ p.add_argument('--organism_part_ref', dest='organism_part_ref', required=False, default="", nargs='?')
+ p.add_argument('--organism_part_iri', dest='organism_part_iri', required=False, default="", nargs='?')
+ p.add_argument('--organism_variant_text', dest='organism_variant_text', required=False, default="", nargs='?')
+ p.add_argument('--organism_variant_ref', dest='organism_variant_ref', required=False, default="", nargs='?')
+ p.add_argument('--organism_variant_iri', dest='organism_variant_iri', required=False, default="", nargs='?')
+
+ args = p.parse_args()
+
+ USERMETA = {'characteristics': {'organism': {'name': '', 'accession': '', 'ref': ''},
+ 'organism_variant': {'name': '', 'accession': '', 'ref': ''},
+ 'organism_part': {'name': '', 'accession': '', 'ref': ''},
+ },
+ 'investigation': {'identifier': '', 'title': 'Investigation', 'description': '',
+ 'submission_date': '', 'release_date': ''
+ },
+ 'investigation_publication': {'pubmed': '', 'doi': '', 'author_list': '', 'title': '',
+ 'status': {'name': '', 'accession': '', 'ref': 'PSO'},
+ },
+
+ 'study': {
+ 'title': '', 'description': '', 'submission_date': '', 'release_date': '',
+ },
+ 'study_publication': {'pubmed': '', 'doi': '', 'author_list': '', 'title': '',
+ 'status': {'name': '', 'accession': '', 'ref': 'PSO'},
+ },
+
+ 'description': {'sample_collect': '', 'extraction': '', 'chroma': '', 'mass_spec': '',
+ 'data_trans': '', 'metabo_id': ''
+ },
+
+ # Multiple Values Parameters
+ 'study_contacts': [
+ {'first_name': '', 'last_name': '', 'mid': '', 'email': '',
+ 'fax': '', 'phone': '', 'adress': '', 'affiliation': '',
+ 'roles': {'name': '', 'accession': '', 'ref': ''},
+ },
+ ],
+
+ 'investigation_contacts': [
+ {'first_name': '', 'last_name': '', 'mid': '', 'email': '',
+ 'fax': '', 'phone': '', 'adress': '', 'affiliation': '',
+ 'roles': {'name': '', 'accession': '', 'ref': ''},
+ },
+ ],
+
+ 'Post Extraction': {'value': ''},
+ 'Derivatization': {'value': ''},
+ 'Chromatography Instrument': {'name': '', 'ref': '', 'accession': ''},
+ 'Column type': {'value': ''},
+ 'Column model': {'value': ''},
+ }
+
+ # check if using json file
+ if args.jsontxt and os.path.isfile(args.jsontxt):
+ with open(args.jsontxt, 'r') as f:
+ USERMETA = json.load(f)
+ else:
+
+ # Fill in USERMETA dictionary
+ USERMETA['characteristics']['organism']['value'] = args.organism_text
+ USERMETA['characteristics']['organism']['accession'] = args.organism_iri
+ USERMETA['characteristics']['organism']['ref'] = args.organism_ref
+
+ USERMETA['characteristics']['organism_variant']['value'] = args.organism_variant_text
+ USERMETA['characteristics']['organism_variant']['accession'] = args.organism_variant_iri
+ USERMETA['characteristics']['organism_variant']['ref'] = args.organism_variant_ref
+
+ USERMETA['characteristics']['organism_part']['value'] = args.organism_part_text
+ USERMETA['characteristics']['organism_part']['accession'] = args.organism_part_iri
+ USERMETA['characteristics']['organism_part']['ref'] = args.organism_part_ref
+
+ # USERMETA['investigation']['identifier'] = # uses study identifier
+ USERMETA['investigation']['description'] = args.i_description
+ USERMETA['investigation']['submission_date'] = args.i_submission_date
+ USERMETA['investigation']['release_date'] = args.i_release_date
+
+ USERMETA['investigation_publication']['pubmed'] = args.i_pubmed
+ USERMETA['investigation_publication']['author_list'] = args.i_pub_author
+ USERMETA['investigation_publication']['title'] = args.i_pub_title
+ USERMETA['investigation_publication']['doi'] = args.i_pub_doi
+ USERMETA['investigation_publication']['status']['name'] = ontology_lookup(args.i_pub_status, 'status')
+ USERMETA['investigation_publication']['status']['accession'] = args.i_pub_status
+
+ USERMETA['investigation_contacts'][0]['first_name'] = args.i_first_name
+ USERMETA['investigation_contacts'][0]['last_name'] = args.i_last_name
+ USERMETA['investigation_contacts'][0]['mid'] = args.i_mid_initials
+ USERMETA['investigation_contacts'][0]['email'] = args.i_mail
+ USERMETA['investigation_contacts'][0]['fax'] = args.i_fax
+ USERMETA['investigation_contacts'][0]['phone'] = args.i_telephone
+ USERMETA['investigation_contacts'][0]['adress'] = args.i_address
+ USERMETA['investigation_contacts'][0]['affiliation'] = args.i_affiliation
+ USERMETA['investigation_contacts'][0]['roles']['name'] = ontology_lookup(args.i_role, 'role')
+ USERMETA['investigation_contacts'][0]['roles']['accession'] = args.i_role
+
+ USERMETA['study']['title'] = args.study_title
+ USERMETA['study']['description'] = args.s_description
+ USERMETA['study']['submission_date'] = args.s_submission_date
+ USERMETA['study']['release_date'] = args.s_release_date
+
+ USERMETA['study_publication']['pubmed'] = args.s_pubmed
+ USERMETA['study_publication']['author_list'] = args.s_pub_author
+ USERMETA['study_publication']['title'] = args.s_pub_title
+ USERMETA['study_publication']['doi'] = args.s_pub_doi
+ USERMETA['study_publication']['status']['name'] = ontology_lookup(args.s_pub_status, 'status')
+ USERMETA['study_publication']['status']['accession'] = args.s_pub_status
+
+ USERMETA['study_contacts'][0]['first_name'] = args.s_first_name
+ USERMETA['study_contacts'][0]['last_name'] = args.s_last_name
+ USERMETA['study_contacts'][0]['mid'] = args.s_mid_initials
+ USERMETA['study_contacts'][0]['email'] = args.s_mail
+ USERMETA['study_contacts'][0]['fax'] = args.s_fax
+ USERMETA['study_contacts'][0]['phone'] = args.s_telephone
+ USERMETA['study_contacts'][0]['adress'] = args.s_address
+ USERMETA['study_contacts'][0]['affiliation'] = args.s_affiliation
+ USERMETA['study_contacts'][0]['roles']['name'] = ontology_lookup(args.s_role, 'role')
+ USERMETA['study_contacts'][0]['roles']['accession'] = args.s_role
+
+
+ try:
+ from mzml2isa.parsing import full_parse
+ # import progressbar as pb
+ # parse the files
+ full_parse(args.inputzip, args.out_dir, args.study_title, usermeta=USERMETA, split=True, merge=False, verbose=True,
+ multip=False)
+
+ except ImportError:
+ import tempfile
+ temp = tempfile.NamedTemporaryFile()
+ temp.write(json.dumps(USERMETA))
+ temp.seek(0)
+ os.system("mzml2isa -i %s -o %s -s %s -m %s" % (args.inputzip, args.out_dir, args.study_title, temp.name))
+ temp.close()
+
+ # The html output is now redundant, the output will be hidden to end user. Have left here in case we need to
+ # revert back to the old output style. If this is the case we need to use
+ # 'wrapper.py -out_dir $html_file.extra_files_path' in the xml code
+ html_code = 'a_%s_metabolite_profiling_mass_spectrometry.txt' \
+ '
i_Investigation.txt
' \
+ 's_test.txt
' % tuple([args.study_title] * 6)
+
+ with open(args.html_file, 'wb') as f:
+ f.write(html_code)
+
+
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r 8f5496765a22 mzml2isa-galaxy-master/packages/package_mzml2isa_0_4_24/shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mzml2isa-galaxy-master/packages/package_mzml2isa_0_4_24/shed.yml Wed Feb 01 10:03:17 2017 -0500
@@ -0,0 +1,10 @@
+name: package_mzml2isa_0_4_19
+owner: rjmweber
+description: Contains a tool dependency definition that downloads and extract version 0.4.19 of mzml2isa.
+homepage_url: https://github.com/ISA-tools/mzml2isa
+long_description: mzml2isa is a Python program that can be used to generate an ISA-Tab structure out of mzML files, providing the backbone of a study which can then be edited with an ISA editing tool (see MetaboLights pre-packaged ISA Creator - http://www.ebi.ac.uk/metabolights/)"
+remote_repository_url: https://github.com/ISA-tools/mzml2isa
+type: tool_dependency_definition
+categories:
+- Tool Dependency Packages
+
diff -r 000000000000 -r 8f5496765a22 mzml2isa-galaxy-master/packages/package_mzml2isa_0_4_24/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mzml2isa-galaxy-master/packages/package_mzml2isa_0_4_24/tool_dependencies.xml Wed Feb 01 10:03:17 2017 -0500
@@ -0,0 +1,22 @@
+
+
+
+
+
+ https://pypi.python.org/packages/bd/bd/1b1e9842eceb80d71d33d65c0b540457f8bcd264f283e81dd7c2d4cb3a30/mzml2isa-0.4.24.zip
+ $INSTALL_DIR/lib/python
+ export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python
+ mzml2isa-0.4.24
+ python setup.py install --install-lib $INSTALL_DIR/lib/python
+
+ $INSTALL_DIR/lib/python
+
+
+
+
+Parser to get meta information from mzML file and parse relevant information to a ISA-Tab structure
+
+https://github.com/ISA-tools/mzml2isa
+
+
+
diff -r 000000000000 -r 8f5496765a22 mzml2isa-galaxy-master/test.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mzml2isa-galaxy-master/test.sh Wed Feb 01 10:03:17 2017 -0500
@@ -0,0 +1,22 @@
+sudo apt-get install python-dev libxml2-dev libxslt1-dev zlib1g-dev
+sudo apt-get install -y python-virtualenv
+virtualenv planemo-venv
+. planemo-venv/bin/activate
+pip install --upgrade pip setuptools
+pip install planemo
+#planemo travis_before_install
+#. .travis/env.sh # source environment created by planemo
+export DOWNLOAD_CACHE=$HOME/download_cache
+mkdir $DOWNLOAD_CACHE
+#git clone https://github.com/ISA-tools/mzml2isa-galaxy.git
+planemo dependency_script -r packages/package_mzml2isa_0_4_22/
+. env.sh
+bash dep_install.sh
+planemo test --galaxy_root=../galaxy galaxy/mzml2isa/
+rm env.sh
+rm dep_install.sh
+deactivate #exit virtualenv
+rm -r planemo-venv
+rm -r lib
+
+