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[Classic Networking] Adding linkouts for MASST+ #732

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[Classic Networking] Adding linkouts for MASST+ #732

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a9d8a28
adding masst linkouts
mwang87 May 21, 2021
a87d7b7
adding masst plus linkouts
mwang87 May 21, 2021
0ad04c3
adding analog search as another option
mwang87 May 21, 2021
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2 changes: 1 addition & 1 deletion metabolomics-snets-v2/Makefile
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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."

15 changes: 14 additions & 1 deletion metabolomics-snets-v2/metabolomics-snets-v2/result.xml
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Expand Up @@ -252,13 +252,26 @@
<parameter name="spectraid" value="[cluster index]"/>
</column>
</row>
<row expander="MASST Spectrum" expandericontype="text">
<row expander="Classic MASST" expandericontype="text">
<column type="singlespectrumcolumnhandler" colspan="5">
<parameter name="mz" value="[precursor mass]"/>
<parameter name="file" file="spectra/specs_ms.mgf"/>
<parameter name="scan" value="[cluster index]"/>
</column>
</row>
<row expander="Advanced MASST" expandericontype="text">
<column label="MASST+" type="genericurlgenerator" width="3" field="cluster index">
<parameter name="URLBASE" value="https://masst.ucsd.edu/masstplus"/>
<parameter name="REQUESTPARAMETER=usi1" value="mzspec:GNPS:TASK-{task}-spectra/specs_ms.mgf:scan:[cluster index]"/>
<parameter name="LABEL" value="MASST+ Search"/>
</column>
<column label="MASST+" type="genericurlgenerator" width="3" field="cluster index">
<parameter name="URLBASE" value="https://masst.ucsd.edu/masstplus"/>
<parameter name="REQUESTPARAMETER=usi1" value="mzspec:GNPS:TASK-{task}-spectra/specs_ms.mgf:scan:[cluster index]"/>
<parameter name="REQUESTPARAMETER=analog" value="Yes"/>
<parameter name="LABEL" value="MASST+ Analog Search"/>
</column>
</row>
<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/"/>\
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