diff --git a/feature-based-molecular-networking/Makefile b/feature-based-molecular-networking/Makefile
index b0d8ae34..e874fe7e 100644
--- a/feature-based-molecular-networking/Makefile
+++ b/feature-based-molecular-networking/Makefile
@@ -3,5 +3,5 @@ include ../Makefile.deploytemplate
WORKFLOW_NAME=feature-based-molecular-networking
TOOL_FOLDER_NAME=feature-based-molecular-networking
-WORKFLOW_VERSION=release_28.2
+WORKFLOW_VERSION=release_31
WORKFLOW_DESCRIPTION='Feature-Based Molecular Networking (FBMN) is a computational method that bridges popular mass spectrometry data processing tools for LC-MS/MS and molecular networking analysis on GNPS. The supported tools are: MZmine, OpenMS, MS-DIAL, MetaboScape, XCMS, Progenesis QI, and the mzTab-M format. FBMN facilitates the detection of isomers that are separated by chromatographic or ion mobility separation, and provides accurate ion abundances for statistical analysis. Note that FBMN requires processing the mass spectrometry data with a feature detection and alignment tool. For rapid/qualitative analysis, we recommend using classical molecular networking that accepts unprocessed mass spectrometry files. See the FBMN documentation at https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking and refer to the "Method and Citation for Manuscripts" on the results page for citations.'
diff --git a/feature-based-molecular-networking/feature-based-molecular-networking/input.xml b/feature-based-molecular-networking/feature-based-molecular-networking/input.xml
index 6ed9389a..d8646f13 100644
--- a/feature-based-molecular-networking/feature-based-molecular-networking/input.xml
+++ b/feature-based-molecular-networking/feature-based-molecular-networking/input.xml
@@ -171,6 +171,7 @@
+
diff --git a/feature-based-molecular-networking/test/reference_input_file_for_formatter/agilent/Checkout_TestMix_AMSMS-MGF.mgf b/feature-based-molecular-networking/test/reference_input_file_for_formatter/agilent/Checkout_TestMix_AMSMS-MGF.mgf
new file mode 100644
index 00000000..f56427d6
--- /dev/null
+++ b/feature-based-molecular-networking/test/reference_input_file_for_formatter/agilent/Checkout_TestMix_AMSMS-MGF.mgf
@@ -0,0 +1,59981 @@
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+END IONS
+BEGIN IONS
+PEPMASS=352.3392656
+CHARGE=1+
+TITLE=Checkout_TestMix_AMSMS.d, MS/MS of 352.3392656 1+ at 12.4597833333333 mins
+RTINSECONDS=747.587
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+END IONS
diff --git a/feature-based-molecular-networking/tools/feature-based-molecular-networking/scripts/agilent_formatter.py b/feature-based-molecular-networking/tools/feature-based-molecular-networking/scripts/agilent_formatter.py
new file mode 100644
index 00000000..cea19ec6
--- /dev/null
+++ b/feature-based-molecular-networking/tools/feature-based-molecular-networking/scripts/agilent_formatter.py
@@ -0,0 +1,42 @@
+
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+@author: Mingxun Wang
+@purpose: to convert the agilent output into a diserable format
+"""
+from io import StringIO
+import pandas as pd
+import sys
+import os
+import ming_spectrum_library
+
+#TODO: Ask about why there are two column headers of the same name
+def convert_to_feature_and_mgf_csv(input_mgf, output_quant, output_mgf):
+ spectrum_collection = ming_spectrum_library.SpectrumCollection(input_mgf)
+ spectrum_collection.load_from_file()
+
+ # Outputting MGF
+ spectrum_collection.make_scans_sequential()
+ spectrum_collection.save_to_mgf(open(output_mgf, "w"))
+
+ output_list = []
+ for spectrum in spectrum_collection.spectrum_list:
+ output_dict = {}
+ output_dict["row ID"] = spectrum.scan
+ output_dict["row m/z"] = spectrum.mz
+ output_dict["row retention time"] = 0
+
+ output_list.append(output_dict)
+
+ df = pd.DataFrame(output_list)
+ df[os.path.basename(input_mgf) + " Peak area"] = 1
+
+ print(df)
+
+ df.to_csv(output_quant, sep=",", index=False)
+
+
+if __name__=="__main__":
+ # there should be obly one input file
+ convert_to_feature_and_mgf_csv(sys.argv[1], sys.argv[2], sys.argv[3])
diff --git a/feature-based-molecular-networking/tools/feature-based-molecular-networking/scripts/reformat_quantification.py b/feature-based-molecular-networking/tools/feature-based-molecular-networking/scripts/reformat_quantification.py
index a5767693..a4af4a6e 100644
--- a/feature-based-molecular-networking/tools/feature-based-molecular-networking/scripts/reformat_quantification.py
+++ b/feature-based-molecular-networking/tools/feature-based-molecular-networking/scripts/reformat_quantification.py
@@ -15,6 +15,7 @@
import mzmine2_formatter
import progenesis_formatter
import mztabm_formatter
+import agilent_formatter
import proteosafe
@@ -115,6 +116,15 @@ def main():
compound_filename_mapping = mztabm_formatter.convert_to_feature_csv(args.quantification_table, args.quantification_table_reformatted)
mztabm_formatter.create_mgf(input_filenames, args.output_mgf, compound_filename_mapping, name_mangle_mapping=name_mangle_mapping)
+ elif args.toolname == "AGILENTMGF":
+ print("AGILENTMGF")
+
+ if len(input_filenames) != 1:
+ print("Must input exactly 1 spectrum mgf file")
+ exit(1)
+
+ input_mgf = input_filenames[0]
+ agilent_formatter.convert_to_feature_and_mgf_csv(input_mgf, args.quantification_table_reformatted, args.output_mgf)
# Finally, we can renormlize the output
try:
diff --git a/qemistree/Makefile b/qemistree/Makefile
index 7f6c0cf5..87be2b43 100644
--- a/qemistree/Makefile
+++ b/qemistree/Makefile
@@ -3,5 +3,5 @@ include ../Makefile.deploytemplate
WORKFLOW_NAME=qemistree
TOOL_FOLDER_NAME=qemistree
-WORKFLOW_VERSION=release_28
+WORKFLOW_VERSION=release_31
WORKFLOW_DESCRIPTION="Qemistree helps you visualize your data by taking into account chemical relationships between the molecules and the quantifications"
diff --git a/qemistree/README.md b/qemistree/README.md
index 37291432..6751e30b 100644
--- a/qemistree/README.md
+++ b/qemistree/README.md
@@ -5,10 +5,21 @@ To install environment, make qiime2-2020.11-qemistree using yml for conda. Then
```
### Updating q2-qemistree
-1. pip uninstall q2-qemistree
-1. pip install https://github.com/biocore/q2-qemistree/archive/2020.1.4.tar.gz
-1. export LC_ALL=en_US.UTF-8 && qiime dev refresh-cache
-1. LC_ALL=en_US.UTF-8 && ./pip install empress
-1. qiime dev refresh-cache
+
+```
+pip uninstall q2-qemistree
+pip install git+https://github.com/biocore/q2-qemistree.git@578f5836cb939b4b27cd602fd5ed0c4fcf08186d
+export LC_ALL=en_US.UTF-8 && qiime dev refresh-cache
+LC_ALL=en_US.UTF-8 && ./pip install empress
+qiime dev refresh-cache
+```
+
+### Installing Sirius
+
+```
+cd tools/qemistree
+wget https://bio.informatik.uni-jena.de/repository/dist-release-local/de/unijena/bioinf/ms/sirius/4.9.3/sirius-4.9.3-linux64-headless.zip
+unzip sirius-4.9.3-linux64-headless.zip
+```
NOTE: Sirius will not work in a branch because it does not tolerate a : in the path
diff --git a/qemistree/qemistree/flow.xml b/qemistree/qemistree/flow.xml
index f5ac64a3..a3950f7c 100755
--- a/qemistree/qemistree/flow.xml
+++ b/qemistree/qemistree/flow.xml
@@ -30,16 +30,16 @@
-
+
-
+
diff --git a/qemistree/qemistree/input.xml b/qemistree/qemistree/input.xml
index f2ea63b6..69e804bc 100755
--- a/qemistree/qemistree/input.xml
+++ b/qemistree/qemistree/input.xml
@@ -41,10 +41,9 @@
-
-
+
diff --git a/qemistree/qemistree/result.xml b/qemistree/qemistree/result.xml
index 59f702ec..bed1807a 100755
--- a/qemistree/qemistree/result.xml
+++ b/qemistree/qemistree/result.xml
@@ -3,7 +3,6 @@
-
@@ -62,7 +61,7 @@
-
+
@@ -75,7 +74,7 @@
-
+
@@ -97,7 +96,7 @@
-
+
diff --git a/qemistree/qemistree/tool.xml b/qemistree/qemistree/tool.xml
index a020d66b..bbd096ae 100755
--- a/qemistree/qemistree/tool.xml
+++ b/qemistree/qemistree/tool.xml
@@ -7,7 +7,7 @@
-
+
diff --git a/qemistree/tools/qemistree/qemistree.py b/qemistree/tools/qemistree/qemistree.py
index c7919824..960c4c8f 100644
--- a/qemistree/tools/qemistree/qemistree.py
+++ b/qemistree/tools/qemistree/qemistree.py
@@ -61,13 +61,27 @@ def main():
cmd = "source {} {} && LC_ALL=en_US.UTF-8 && export LC_ALL && qiime tools import --input-path {} --output-path {} --type MassSpectrometryFeatures".format(args.conda_activate_bin, args.conda_environment, args.input_sirius_mgf, output_mgf_qza)
all_cmd.append(cmd)
+ ions_considered = ""
+ if args.ionization_mode == "positive":
+ ions_considered = "[M+H]+"
+ elif args.ionization_mode == "negative":
+ ions_considered = "[M-H]-"
+
+
cmd = 'source {} {} && LC_ALL=en_US.UTF-8 && export LC_ALL && qiime qemistree compute-fragmentation-trees --p-sirius-path {} \
--i-features {} \
--p-ppm-max {} \
--p-profile {} \
- --p-ionization-mode {} \
+ --p-ions-considered "{}" \
--p-java-flags "-Djava.io.tmpdir=./temp -Xms16G -Xmx64G" \
- --o-fragmentation-trees {}'.format(args.conda_activate_bin, args.conda_environment, args.sirius_bin, output_mgf_qza, ppm_max, instrument, args.ionization_mode, output_fragtree_qza)
+ --o-fragmentation-trees {}'.format(args.conda_activate_bin, \
+ args.conda_environment, \
+ args.sirius_bin, \
+ output_mgf_qza, \
+ ppm_max, \
+ instrument, \
+ ions_considered, \
+ output_fragtree_qza)
all_cmd.append(cmd)
cmd = 'source {} {} && LC_ALL=en_US.UTF-8 && export LC_ALL && qiime qemistree rerank-molecular-formulas --p-sirius-path {} \
@@ -81,6 +95,7 @@ def main():
cmd = 'source {} {} && LC_ALL=en_US.UTF-8 && export LC_ALL && qiime qemistree predict-fingerprints --p-sirius-path {} \
--i-molecular-formulas {} \
--p-ppm-max {} \
+ --p-fingerid-db "all" \
--p-java-flags "-Djava.io.tmpdir=./temp -Xms16G -Xmx64G" \
--o-predicted-fingerprints {}'.format(args.conda_activate_bin, args.conda_environment, args.sirius_bin, output_formula_qza, ppm_max, output_fingerprints_qza)
all_cmd.append(cmd)
@@ -180,7 +195,8 @@ def main():
--m-feature-metadata-file {output_classified_feature_data_qza} \
--m-sample-metadata-file {metadata_files[0]} \
--o-visualization {output_qemistree_empress_qzv} \
- --p-filter-missing-features'
+ --p-filter-missing-features \
+ --p-ignore-missing-samples'
all_cmd.append(cmd)
# saving sample metadata
diff --git a/qemistree/tools/qemistree/sirius-linux64-4.0.1/bin/COPYING.txt b/qemistree/tools/qemistree/sirius-linux64-4.0.1/bin/COPYING.txt
deleted file mode 100644
index 93ba659f..00000000
--- a/qemistree/tools/qemistree/sirius-linux64-4.0.1/bin/COPYING.txt
+++ /dev/null
@@ -1,689 +0,0 @@
---------------------------------------------------------------------------
-SIRIUS -- MS and MS/MS analyzing software
---------------------------------------------------------------------------
-Copyright Kai Dührkop and the SIRIUS developer team at Chair of Bioinformatics,
-Friedrich-Schilller University Jena 2013-2015.
-
-This software is distributed together with the GLPK (GNU Linear Programing Kit)
-library, which is licenced under GPL. Its source code is available under
-http://ftp.gnu.org/gnu/glpk/
-
-Please follow the terms and conditions of GPL when distributing SIRIUS together
-with the GLPK library.
----------------------------------------------------------------------------
-
-
- GNU GENERAL PUBLIC LICENSE
- Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc.
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
- Preamble
-
- The GNU General Public License is a free, copyleft license for
-software and other kinds of works.
-
- The licenses for most software and other practical works are designed
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\ No newline at end of file
diff --git a/qemistree/tools/qemistree/sirius-linux64-4.0.1/bin/LICENSE.txt b/qemistree/tools/qemistree/sirius-linux64-4.0.1/bin/LICENSE.txt
deleted file mode 100644
index 20d40b6b..00000000
--- a/qemistree/tools/qemistree/sirius-linux64-4.0.1/bin/LICENSE.txt
+++ /dev/null
@@ -1,674 +0,0 @@
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-Program specifies that a certain numbered version of the GNU General
-Public License "or any later version" applies to it, you have the
-option of following the terms and conditions either of that numbered
-version or of any later version published by the Free Software
-Foundation. If the Program does not specify a version number of the
-GNU General Public License, you may choose any version ever published
-by the Free Software Foundation.
-
- If the Program specifies that a proxy can decide which future
-versions of the GNU General Public License can be used, that proxy's
-public statement of acceptance of a version permanently authorizes you
-to choose that version for the Program.
-
- Later license versions may give you additional or different
-permissions. However, no additional obligations are imposed on any
-author or copyright holder as a result of your choosing to follow a
-later version.
-
- 15. Disclaimer of Warranty.
-
- THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
-APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
-HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
-OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
-THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
-IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
-ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
-
- 16. Limitation of Liability.
-
- IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
-THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
-GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
-USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
-DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
-PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
-EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGES.
-
- 17. Interpretation of Sections 15 and 16.
-
- If the disclaimer of warranty and limitation of liability provided
-above cannot be given local legal effect according to their terms,
-reviewing courts shall apply local law that most closely approximates
-an absolute waiver of all civil liability in connection with the
-Program, unless a warranty or assumption of liability accompanies a
-copy of the Program in return for a fee.
-
- END OF TERMS AND CONDITIONS
-
- How to Apply These Terms to Your New Programs
-
- If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
- To do so, attach the following notices to the program. It is safest
-to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
-
- Copyright (C)
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see .
-
-Also add information on how to contact you by electronic and paper mail.
-
- If the program does terminal interaction, make it output a short
-notice like this when it starts in an interactive mode:
-
- Copyright (C)
- This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
- This is free software, and you are welcome to redistribute it
- under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License. Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
-
- You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
-.
-
- The GNU General Public License does not permit incorporating your program
-into proprietary programs. If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library. If this is what you want to do, use the GNU Lesser General
-Public License instead of this License. But first, please read
-.
\ No newline at end of file
diff --git a/qemistree/tools/qemistree/sirius-linux64-4.0.1/bin/sirius b/qemistree/tools/qemistree/sirius-linux64-4.0.1/bin/sirius
deleted file mode 100755
index 14d6112e..00000000
--- a/qemistree/tools/qemistree/sirius-linux64-4.0.1/bin/sirius
+++ /dev/null
@@ -1,174 +0,0 @@
-#!/usr/bin/env sh
-
-##############################################################################
-##
-## sirius start up script for UN*X
-##
-##############################################################################
-
-# Attempt to set APP_HOME
-# Resolve links: $0 may be a link
-PRG="$0"
-# Need this for relative symlinks.
-while [ -h "$PRG" ] ; do
- ls=`ls -ld "$PRG"`
- link=`expr "$ls" : '.*-> \(.*\)$'`
- if expr "$link" : '/.*' > /dev/null; then
- PRG="$link"
- else
- PRG=`dirname "$PRG"`"/$link"
- fi
-done
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/.." >/dev/null
-APP_HOME="`pwd -P`"
-cd "$SAVED" >/dev/null
-
-APP_NAME="sirius"
-APP_BASE_NAME=`basename "$0"`
-
-export LD_LIBRARY_PATH="$GUROBI_HOME/lib:$CPLEX_HOME/bin/x86-64_linux:$CPLEX_HOME/bin/x86-64_osx:$CPLEX_HOME/bin/x64_win64:$CPLEX_HOME/bin/x86_win32:$APP_HOME/lib:$LD_LIBRARY_PATH"
-export DYLD_LIBRARY_PATH="$LD_LIBRARY_PATH"
-# Add default JVM options here. You can also use JAVA_OPTS and SIRIUS_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS="-Djava.library.path=\"$GUROBI_HOME/lib:$CPLEX_HOME/bin/x86-64_linux:$CPLEX_HOME/bin/x86-64_osx:$CPLEX_HOME/bin/x64_win64:$CPLEX_HOME/bin/x86_win32:$APP_HOME/lib\""
-
-# Use the maximum available, or set MAX_FD != -1 to use that value.
-MAX_FD="maximum"
-
-warn ( ) {
- echo "$*"
-}
-
-die ( ) {
- echo
- echo "$*"
- echo
- exit 1
-}
-
-# OS specific support (must be 'true' or 'false').
-cygwin=false
-msys=false
-darwin=false
-nonstop=false
-case "`uname`" in
- CYGWIN* )
- cygwin=true
- ;;
- Darwin* )
- darwin=true
- ;;
- MINGW* )
- msys=true
- ;;
- NONSTOP* )
- nonstop=true
- ;;
-esac
-
-CLASSPATH="${GUROBI_HOME}/lib/gurobi.jar:${CPLEX_HOME}/lib/cplex.jar:$APP_HOME/lib/sirius_gui-4.0.1.jar:$APP_HOME/lib/trove4j-3.0.3.jar:$APP_HOME/lib/guava-18.0.jar:$APP_HOME/lib/sirius_cli-4.0.1.jar:$APP_HOME/lib/jjobs-swing-0.9.6.jar:$APP_HOME/lib/javax.json-api-1.0.jar:$APP_HOME/lib/javax.json-1.0.4.jar:$APP_HOME/lib/opencsv-2.3.jar:$APP_HOME/lib/swingx-all-1.6.5-1.jar:$APP_HOME/lib/cdk-render-2.1.1.jar:$APP_HOME/lib/cdk-renderextra-2.1.1.jar:$APP_HOME/lib/cdk-renderawt-2.1.1.jar:$APP_HOME/lib/cdk-data-2.1.1.jar:$APP_HOME/lib/cdk-core-2.1.1.jar:$APP_HOME/lib/cdk-interfaces-2.1.1.jar:$APP_HOME/lib/cdk-inchi-2.1.1.jar:$APP_HOME/lib/cdk-smiles-2.1.1.jar:$APP_HOME/lib/cdk-io-2.1.1.jar:$APP_HOME/lib/cdk-ioformats-2.1.1.jar:$APP_HOME/lib/cdk-sdg-2.1.1.jar:$APP_HOME/lib/cdk-smarts-2.1.1.jar:$APP_HOME/lib/glazedlists_java16-1.10.0.jar:$APP_HOME/lib/jewelcli-0.8.9.jar:$APP_HOME/lib/sirius_api-4.0.1.jar:$APP_HOME/lib/slf4j-jdk14-1.7.25.jar:$APP_HOME/lib/httpclient-4.5.1.jar:$APP_HOME/lib/gibbs_sampling-4.0.1.jar:$APP_HOME/lib/error-reporter-0.9.2.jar:$APP_HOME/lib/classpath-explorer-1.0.jar:$APP_HOME/lib/fingerid_db_oss-1.1.3.jar:$APP_HOME/lib/fingerprinter_oss-1.1.3.jar:$APP_HOME/lib/fingerblast_oss-1.1.3.jar:$APP_HOME/lib/chemdb_rest_oss-1.1.3.jar:$APP_HOME/lib/chemdb_file_oss-1.1.3.jar:$APP_HOME/lib/chemical_db_oss-1.1.3.jar:$APP_HOME/lib/canopus_predict_oss-1.1.3.jar:$APP_HOME/lib/maven-artifact-3.5.0.jar:$APP_HOME/lib/base64-2.3.8.jar:$APP_HOME/lib/cdk-silent-2.1.1.jar:$APP_HOME/lib/annotations-15.0.jar:$APP_HOME/lib/jjobs-core-0.9.6.jar:$APP_HOME/lib/vecmath-1.5.2.jar:$APP_HOME/lib/cdk-standard-2.1.1.jar:$APP_HOME/lib/cdk-renderbasic-2.1.1.jar:$APP_HOME/lib/jni-inchi-0.8.jar:$APP_HOME/lib/beam-core-1.1.jar:$APP_HOME/lib/beam-func-1.1.jar:$APP_HOME/lib/cdk-valencycheck-2.1.1.jar:$APP_HOME/lib/cdk-atomtype-2.1.1.jar:$APP_HOME/lib/cdk-isomorphism-2.1.1.jar:$APP_HOME/lib/cdk-ctab-2.1.1.jar:$APP_HOME/lib/chemistry_base-4.0.1.jar:$APP_HOME/lib/io-4.0.1.jar:$APP_HOME/lib/isotope_pattern_analysis-4.0.1.jar:$APP_HOME/lib/fragmentation_tree_construction-4.0.1.jar:$APP_HOME/lib/httpcore-4.4.3.jar:$APP_HOME/lib/commons-logging-1.2.jar:$APP_HOME/lib/commons-codec-1.9.jar:$APP_HOME/lib/cdk-formula-2.1.1.jar:$APP_HOME/lib/gson-2.6.2.jar:$APP_HOME/lib/commons-email-1.4.jar:$APP_HOME/lib/oshi-core-3.4.4.jar:$APP_HOME/lib/fingerid_utils_oss-1.1.3.jar:$APP_HOME/lib/chemdb_sql_oss-1.1.3.jar:$APP_HOME/lib/cdk-fingerprint-2.1.1.jar:$APP_HOME/lib/cdk-qsarmolecular-2.1.1.jar:$APP_HOME/lib/cdk-qsaratomic-2.1.1.jar:$APP_HOME/lib/json-1.0.jar:$APP_HOME/lib/fingerprint_pvalues_oss-1.1.3.jar:$APP_HOME/lib/ejml-fdense-0.31.jar:$APP_HOME/lib/ejml-simple-0.31.jar:$APP_HOME/lib/plexus-utils-3.0.24.jar:$APP_HOME/lib/commons-lang3-3.5.jar:$APP_HOME/lib/jnati-deploy-0.4.jar:$APP_HOME/lib/GraphUtils-1.1.jar:$APP_HOME/lib/mass_decomposer-4.0.1.jar:$APP_HOME/lib/commons-math3-3.6.1.jar:$APP_HOME/lib/Recalibration-1.0.jar:$APP_HOME/lib/glpk-java-1.7.0.jar:$APP_HOME/lib/gurobi-linux64-7.5.2.jar:$APP_HOME/lib/cplex-12.8.jar:$APP_HOME/lib/javax.mail-1.5.2.jar:$APP_HOME/lib/activation-1.1.1.jar:$APP_HOME/lib/jna-platform-4.5.0.jar:$APP_HOME/lib/threetenbp-1.3.6.jar:$APP_HOME/lib/postgresql-42.2.1.jar:$APP_HOME/lib/jama-1.0.3.jar:$APP_HOME/lib/xom-1.2.5.jar:$APP_HOME/lib/cdk-reaction-2.1.1.jar:$APP_HOME/lib/cdk-charges-2.1.1.jar:$APP_HOME/lib/cdk-qsar-2.1.1.jar:$APP_HOME/lib/cdk-dict-2.1.1.jar:$APP_HOME/lib/cdk-fragment-2.1.1.jar:$APP_HOME/lib/cdk-hash-2.1.1.jar:$APP_HOME/lib/cdk-forcefield-2.1.1.jar:$APP_HOME/lib/ejml-core-0.31.jar:$APP_HOME/lib/ejml-ddense-0.31.jar:$APP_HOME/lib/jnati-core-0.4.jar:$APP_HOME/lib/log4j-1.2.14.jar:$APP_HOME/lib/java-utilities-1.0-SNAPSHOT.jar:$APP_HOME/lib/javatuples-1.3-SNAPSHOT.jar:$APP_HOME/lib/jna-4.5.0.jar:$APP_HOME/lib/xercesImpl-2.8.0.jar:$APP_HOME/lib/xalan-2.7.0.jar:$APP_HOME/lib/slf4j-api-1.7.25.jar:$APP_HOME/lib/xml-apis-2.0.2.jar"
-
-# Determine the Java command to use to start the JVM.
-if [ -n "$JAVA_HOME" ] ; then
- if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
- # IBM's JDK on AIX uses strange locations for the executables
- JAVACMD="$JAVA_HOME/jre/sh/java"
- else
- JAVACMD="$JAVA_HOME/bin/java"
- fi
- if [ ! -x "$JAVACMD" ] ; then
- die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
-
-Please set the JAVA_HOME variable in your environment to match the
-location of your Java installation."
- fi
-else
- JAVACMD="java"
- which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-
-Please set the JAVA_HOME variable in your environment to match the
-location of your Java installation."
-fi
-
-# Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
- MAX_FD_LIMIT=`ulimit -H -n`
- if [ $? -eq 0 ] ; then
- if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
- MAX_FD="$MAX_FD_LIMIT"
- fi
- ulimit -n $MAX_FD
- if [ $? -ne 0 ] ; then
- warn "Could not set maximum file descriptor limit: $MAX_FD"
- fi
- else
- warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
- fi
-fi
-
-# For Darwin, add options to specify how the application appears in the dock
-if $darwin; then
- GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
-fi
-
-# For Cygwin, switch paths to Windows format before running java
-if $cygwin ; then
- APP_HOME=`cygpath --path --mixed "$APP_HOME"`
- CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
- JAVACMD=`cygpath --unix "$JAVACMD"`
-
- # We build the pattern for arguments to be converted via cygpath
- ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
- SEP=""
- for dir in $ROOTDIRSRAW ; do
- ROOTDIRS="$ROOTDIRS$SEP$dir"
- SEP="|"
- done
- OURCYGPATTERN="(^($ROOTDIRS))"
- # Add a user-defined pattern to the cygpath arguments
- if [ "$GRADLE_CYGPATTERN" != "" ] ; then
- OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
- fi
- # Now convert the arguments - kludge to limit ourselves to /bin/sh
- i=0
- for arg in "$@" ; do
- CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
- CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option
-
- if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition
- eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
- else
- eval `echo args$i`="\"$arg\""
- fi
- i=$((i+1))
- done
- case $i in
- (0) set -- ;;
- (1) set -- "$args0" ;;
- (2) set -- "$args0" "$args1" ;;
- (3) set -- "$args0" "$args1" "$args2" ;;
- (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
- (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
- (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
- (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
- (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
- (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
- esac
-fi
-
-# Escape application args
-save ( ) {
- for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
- echo " "
-}
-APP_ARGS=$(save "$@")
-
-# Collect all arguments for the java command, following the shell quoting and substitution rules
-eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $SIRIUS_OPTS -classpath "\"$CLASSPATH\"" de.unijena.bioinf.ms.cli.SiriusGUIApplication "$APP_ARGS"
-
-# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
-if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
- cd "$(dirname "$0")"
-fi
-
-exec "$JAVACMD" "$@"
\ No newline at end of file
diff --git a/qemistree/tools/qemistree/sirius-linux64-4.0.1/bin/sirius-gui b/qemistree/tools/qemistree/sirius-linux64-4.0.1/bin/sirius-gui
deleted file mode 100755
index f8879643..00000000
--- a/qemistree/tools/qemistree/sirius-linux64-4.0.1/bin/sirius-gui
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env bash
-
-# get the absolute path of the executable
-SELF_PATH="$(cd -P -- "$(dirname -- "$0")" && pwd -P)" && SELF_PATH="$SELF_PATH"/$(basename -- "$0")
-# resolve symlinks
-while [ -h "$SELF_PATH" ]; do
- # 1) cd to directory of the symlink
- # 2) cd to the directory of where the symlink points
- # 3) get the pwd
- # 4) append the basename
- DIR=$(dirname -- "$SELF_PATH")
- SYM=$(readlink "$SELF_PATH")
- SELF_PATH=$(cd "$DIR" && cd $(dirname -- "$SYM") && pwd)/$(basename -- "$SYM")
-done
-
-if [ -z "$SELF_PATH" ]; then
- APP_HOME=$(dirname "$0")
-else
- APP_HOME=$(dirname "$SELF_PATH")
-fi
-
-"$APP_HOME"/sirius --gui
diff --git a/qemistree/tools/qemistree/sirius-linux64-4.0.1/bin/sirius.ico b/qemistree/tools/qemistree/sirius-linux64-4.0.1/bin/sirius.ico
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diff --git a/qemistree/tools/qemistree/sirius-linux64-4.0.1/doc/sirius-4.0.1-manual.pdf b/qemistree/tools/qemistree/sirius-linux64-4.0.1/doc/sirius-4.0.1-manual.pdf
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diff --git a/qemistree/tools/qemistree/sirius-linux64-4.0.1/lib/cdk-atomtype-2.1.1.jar b/qemistree/tools/qemistree/sirius-linux64-4.0.1/lib/cdk-atomtype-2.1.1.jar
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diff --git a/qemistree/tools/qemistree/sirius-linux64-4.0.1/lib/cdk-charges-2.1.1.jar b/qemistree/tools/qemistree/sirius-linux64-4.0.1/lib/cdk-charges-2.1.1.jar
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diff --git a/qemistree/tools/qemistree/summarize_fingerprint.py b/qemistree/tools/qemistree/summarize_fingerprint.py
index 14200928..caac801b 100644
--- a/qemistree/tools/qemistree/summarize_fingerprint.py
+++ b/qemistree/tools/qemistree/summarize_fingerprint.py
@@ -21,38 +21,38 @@ def main():
os.system(cmd)
#Loading fingerprint mapping
- fingerprint_mapping_filenames = glob.glob("**/data/csi-output/fingerprints.csv", recursive=True)
- fingerprint_mapping = {}
- if len(fingerprint_mapping_filenames) == 1:
- df = pd.read_csv(fingerprint_mapping_filenames[0], sep="\t")
- for fingerprint_record in df.to_dict(orient="records"):
- index = fingerprint_record["relativeIndex"]
- description = fingerprint_record["description"]
- fingerprint_mapping[index] = description
-
- #Loading all the actual fingerprints
- output_fingerprint_summary_list = []
- all_features_folder = glob.glob("**/csi-output/*_features_*", recursive=True)
- for feature_folder in all_features_folder:
- fingerprint_filenames = glob.glob(os.path.join(feature_folder, "fingerprints/*.fpt"))
- if len(fingerprint_filenames) != 1:
- continue
-
- feature_id = os.path.basename(feature_folder).split("_")[0]
-
- feature_dict = {}
- feature_dict["feature_id"] = feature_id
-
- i = 0
- for line in open(fingerprint_filenames[0]):
- fingerprint_value = float(line.rstrip())
- fingerprint_name = fingerprint_mapping[i]
- feature_dict["FINGERPRINT_{}".format(fingerprint_name)] = fingerprint_value
- i += 1
-
- output_fingerprint_summary_list.append(feature_dict)
-
- pd.DataFrame(output_fingerprint_summary_list).to_csv(os.path.join(args.summary_folder, "summary_fingerprints.tsv"), sep="\t", index=False)
+ # fingerprint_mapping_filenames = glob.glob("**/data/csi-output/fingerprints.csv", recursive=True)
+ # fingerprint_mapping = {}
+ # if len(fingerprint_mapping_filenames) == 1:
+ # df = pd.read_csv(fingerprint_mapping_filenames[0], sep="\t")
+ # for fingerprint_record in df.to_dict(orient="records"):
+ # index = fingerprint_record["relativeIndex"]
+ # description = fingerprint_record["description"]
+ # fingerprint_mapping[index] = description
+
+ # #Loading all the actual fingerprints
+ # output_fingerprint_summary_list = []
+ # all_features_folder = glob.glob("**/csi-output/*_features_*", recursive=True)
+ # for feature_folder in all_features_folder:
+ # fingerprint_filenames = glob.glob(os.path.join(feature_folder, "fingerprints/*.fpt"))
+ # if len(fingerprint_filenames) != 1:
+ # continue
+
+ # feature_id = os.path.basename(feature_folder).split("_")[0]
+
+ # feature_dict = {}
+ # feature_dict["feature_id"] = feature_id
+
+ # i = 0
+ # for line in open(fingerprint_filenames[0]):
+ # fingerprint_value = float(line.rstrip())
+ # fingerprint_name = fingerprint_mapping[i]
+ # feature_dict["FINGERPRINT_{}".format(fingerprint_name)] = fingerprint_value
+ # i += 1
+
+ # output_fingerprint_summary_list.append(feature_dict)
+
+ # pd.DataFrame(output_fingerprint_summary_list).to_csv(os.path.join(args.summary_folder, "summary_fingerprints.tsv"), sep="\t", index=False)
#Parsing out the classified summary
input_csi_qza = os.path.join(args.results_folder, "classified-feature-data.qza")