Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[Classic Networking] Adding new binary for listing out peak matches and min ratio #729

Draft
wants to merge 3 commits into
base: master
Choose a base branch
from
Draft

[Classic Networking] Adding new binary for listing out peak matches and min ratio #729

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
57f49b9
adding new binary
mwang87 May 12, 2021
e38cecf
changing the min ratio to 0.01
mwang87 May 21, 2021
8acdb0c
updating parameters
mwang87 May 21, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion metabolomics-snets-v2/Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,6 @@ include ../Makefile.deploytemplate

WORKFLOW_NAME=metabolomics-snets-v2
TOOL_FOLDER_NAME=metabolomicsnetsv2
WORKFLOW_VERSION=release_28.2
WORKFLOW_VERSION=release_29
WORKFLOW_DESCRIPTION="Molecular networks are visual displays of the chemical space present in tandem mass spectrometry (MS/MS) experiments. This visualization approach can detect sets of spectra from related molecules (molecular networks), even when the spectra themselves are not matched to any known compounds. Classical molecular networking is well suited for discovery and can be analyzed directly from raw mass spectrometry files. Feature-based Molecular Networking (FBMN) is better when quantification analysis is necessary, but requires preprocessing with feature finding tools."

22 changes: 22 additions & 0 deletions metabolomics-snets-v2/metabolomics-snets-v2/input.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,11 @@
<validator type="integer" minimumExclusive="0" maximum="500"/>
</parameter>

<parameter name="MIN_RATIO" label="Minimum Explained Aligned Intensity Ratio">
<default value="0.4"/>
<validator type="float" minimumExclusive="0" maximum="1"/>
</parameter>


<parameter name="TOPK" label="Network TopK">
<default value="10"/>
Expand Down Expand Up @@ -421,6 +426,7 @@
</cell>
</row>
</block>

<block label="Advanced Network Options">
<row>
<cell>
Expand Down Expand Up @@ -452,6 +458,22 @@
</cell>
</row>

<row>
<cell>
<label>
<content parameter="MIN_RATIO"/>
<tooltip id="min_pair_cosine_tooltip">
Minimum cosine score that must occur between a pair of consensus MS/MS spectra in order for an edge to be formed in the molecular network. Default value is 0.7. Lower value will increase the size of the clusters by inducing the clustering of less related MS/MS spectra, higher value will limit do the opposite.
</tooltip>
</label>
</cell>
<cell>
<input type="text" parameter="MIN_RATIO">
<attribute name="size" value="3"/>
</input>
</cell>
</row>

<row>
<cell>
<label>
Expand Down
Binary file modified metabolomics-snets-v2/tools/metabolomicsnetsv2/binaries/main_execmodule
View file
Open in desktop
Binary file not shown.
2 changes: 1 addition & 1 deletion ...olomics-snets-v2/tools/metabolomicsnetsv2/scripts/prep_molecular_networking_parameters.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ def main():
output_parameter_file.write("PAIRS_MIN_COSINE=%s\n" % (params_object["PAIRS_MIN_COSINE"][0]))
#output_parameter_file.write("MAX_SHIFT=%s\n" % (params_object["MAX_SHIFT"][0]))
output_parameter_file.write("MAX_SHIFT=%s\n" % ("9999"))
output_parameter_file.write("MIN_RATIO=%s\n" % ("0.4"))
output_parameter_file.write("MIN_RATIO=%s\n" % (params_object["MIN_RATIO"][0]))
output_parameter_file.write("INPUT_SPECTRA_MS2=%s\n" % (args.mgf_filename))


Expand Down