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FBMN new dashboard for plotting #600

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merged 4 commits into from
Aug 25, 2020
Merged

FBMN new dashboard for plotting #600

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496efd0
bumping version
mwang87 Aug 23, 2020
947786a
updating linkouts
mwang87 Aug 23, 2020
49c7c72
adding linkouts
mwang87 Aug 25, 2020
b280a0d
adding a beta tag
mwang87 Aug 25, 2020
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2 changes: 1 addition & 1 deletion feature-based-molecular-networking/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,5 @@ include ../Makefile.deploytemplate

WORKFLOW_NAME=feature-based-molecular-networking
TOOL_FOLDER_NAME=feature-based-molecular-networking
WORKFLOW_VERSION=release_23
WORKFLOW_VERSION=release_25
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.'
19 changes: 12 additions & 7 deletions feature-based-molecular-networking/feature-based-molecular-networking/result.xml
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Expand Up @@ -262,7 +262,6 @@
<parameter name="VALUE_TO_CONSIDER" value="[componentindex]"/>
</column>


<column label="AnnotatetoGNPS" type="genericurlgenerator" width="10">
<parameter name="URLBASE" value="/ProteoSAFe/index.jsp"/>
<parameter name="HASHPARAMTER=workflow" value="ADD-SINGLE-ANNOTATED-BRONZE"/>
Expand All @@ -271,6 +270,12 @@
<parameter name="LABEL" value="AnnotatetoGNPS"/>
</column>

<column type="genericurlgenerator" label="Quant">
<parameter name="URLBASE" value="http://dorresteintesthub.ucsd.edu:6549"/>
<parameter name="LABEL" value="Quant Plots (Beta)"/>
<parameter name="REQUESTPARAMETER=feature" value="[cluster index]"/>
<parameter name="USETASK" value="True"/>
</column>


<column type="float" field="precursor mass" label="PrecursorMZ" precision="5"/>
Expand Down Expand Up @@ -639,7 +644,7 @@
<parameter name="USETASK" value="True"/>
</column>
<column type="genericurlgenerator" label="Customize Plotting">
<parameter name="URLBASE" value="http://dorresteintesthub.ucsd.edu:8347"/>
<parameter name="URLBASE" value="http://dorresteintesthub.ucsd.edu:6549"/>
<parameter name="LABEL" value="Customize Plot"/>
<parameter name="REQUESTPARAMETER=feature" value="[scan]"/>
<parameter name="USETASK" value="True"/>
Expand Down Expand Up @@ -675,7 +680,7 @@
<parameter name="USETASK" value="True"/>
</column>
<column type="genericurlgenerator" label="Customize Plotting">
<parameter name="URLBASE" value="http://dorresteintesthub.ucsd.edu:8347"/>
<parameter name="URLBASE" value="http://dorresteintesthub.ucsd.edu:6549"/>
<parameter name="LABEL" value="Customize Plot"/>
<parameter name="REQUESTPARAMETER=feature" value="[scan]"/>
<parameter name="USETASK" value="True"/>
Expand All @@ -690,16 +695,16 @@
</row>
</block>

<view id="esquisse_data_for_plotting" label="Data Exploration with Esquisse/ggplot2" group="Advanced Views - Stats Views (Experimental)">
<blockRef id="main" type="esquisse_data_for_plotting"/>
<view id="interactive_data_for_plotting" label="Data Exploration with Interactive Plotting" group="Advanced Views - Stats Views (Experimental)">
<blockRef id="main" type="interactive_data_for_plotting"/>
</view>
<block id="esquisse_data_for_plotting" type="dummylinkout">
<block id="interactive_data_for_plotting" type="dummylinkout">
<data>
<parsers>
<parser type="stream" contentType="text/xml"/>
</parsers>
</data>
<parameter name="URLBASE" value='http://dorresteintesthub.ucsd.edu:8347?task=[task]'/>
<parameter name="URLBASE" value='http://dorresteintesthub.ucsd.edu:6549?task=[task]'/>
</block>

<view id="data_for_plotting" label="API Data for Plotting" group="Advanced Views - Stats Views (Experimental)">
Expand Down