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

Classical Networking New USI Identifiers #590

Merged
merged 2 commits into from
Aug 4, 2020
Merged

Classical Networking New USI Identifiers #590

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
e048df7
switching to use new USI identifiers
mwang87 Aug 4, 2020
5042d28
slight bug fix for usi link
mwang87 Aug 4, 2020
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_23
WORKFLOW_VERSION=release_25
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."

12 changes: 6 additions & 6 deletions metabolomics-snets-v2/metabolomics-snets-v2/result.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -103,18 +103,18 @@
<row expander="USI Links" expandericontype="text">
<column label="USI-Spectrum" type="genericurlgenerator" width="3"> \
<parameter name="URLBASE" value="https://metabolomics-usi.ucsd.edu/mirror/"/>\
<parameter name="REQUESTPARAMETER=usi1" value="mzspec:GNPSTASK-{task}:spectra/specs_ms.mgf:scan:[#Scan#]"/>
<parameter name="REQUESTPARAMETER=usi2" value="mzspec:GNPSLIBRARY:[SpectrumID]"/>
<parameter name="REQUESTPARAMETER=usi1" value="mzspec:GNPS:TASK-{task}-spectra/specs_ms.mgf:scan:[#Scan#]"/>
<parameter name="REQUESTPARAMETER=usi2" value="mzspec:GNPS:GNPS-LIBRARY:accession:[SpectrumID]"/>
<parameter name="LABEL" value="Mirror Match USI"/>
</column>
<column label="USI-Spectrum" type="genericurlgenerator" width="3"> \
<parameter name="URLBASE" value="https://metabolomics-usi.ucsd.edu/spectrum/"/>\
<parameter name="REQUESTPARAMETER=usi" value="mzspec:GNPSTASK-{task}:spectra/specs_ms.mgf:scan:[#Scan#]"/>
<parameter name="REQUESTPARAMETER=usi" value="mzspec:GNPS:TASK-{task}-spectra/specs_ms.mgf:scan:[#Scan#]"/>
<parameter name="LABEL" value="Query Spectrum USI"/>
</column>
<column label="USI-Library" type="genericurlgenerator" width="3"> \
<parameter name="URLBASE" value="https://metabolomics-usi.ucsd.edu/spectrum/"/>\
<parameter name="REQUESTPARAMETER=usi" value="mzspec:GNPSLIBRARY:[SpectrumID]"/>
<parameter name="REQUESTPARAMETER=usi" value="mzspec:GNPS:GNPS-LIBRARY:accession:[SpectrumID]"/>
<parameter name="LABEL" value="Library Spectrum USI"/>
</column>
</row>
Expand Down Expand Up @@ -255,7 +255,7 @@
<row expander="USI Links" expandericontype="text">
<column label="USI-Spectrum" type="genericurlgenerator" width="3" field="cluster index"> \
<parameter name="URLBASE" value="https://metabolomics-usi.ucsd.edu/spectrum/"/>\
<parameter name="REQUESTPARAMETER=usi" value="mzspec:GNPSTASK-{task}:spectra/specs_ms.mgf:scan:[cluster index]"/>
<parameter name="REQUESTPARAMETER=usi" value="mzspec:GNPS:TASK-{task}-spectra/specs_ms.mgf:scan:[cluster index]"/>
<parameter name="LABEL" value="Spectrum USI"/>
</column>
</row>
Expand Down Expand Up @@ -1125,7 +1125,7 @@
<row expander="USI Links" expandericontype="text">
<column label="USI-Spectrum" type="genericurlgenerator" width="3"> \
<parameter name="URLBASE" value="https://metabolomics-usi.ucsd.edu/spectrum/"/>\
<parameter name="REQUESTPARAMETER=usi" value="mzspec:GNPSTASK-{task}:[Original_Path]:scan:[ScanNumber]"/>
<parameter name="REQUESTPARAMETER=usi" value="mzspec:GNPS:TASK-{task}-[Original_Path]:scan:[ScanNumber]"/>
<parameter name="LABEL" value="Spectrum USI"/>
</column>
</row>
Expand Down