From e9f4290c3f0640ddcfeb8bbc4a5611701c877af5 Mon Sep 17 00:00:00 2001
From: Mingxun Wang <mwang87@gmail.com>
Date: Tue, 29 Jun 2021 09:47:54 -0700
Subject: [PATCH 1/2] adding user defined parameter for the level of
 parallelism we could allow

---
 metabolomics-snets-v2/Makefile                |  2 +-
 .../metabolomics-snets-v2/input.xml           | 24 +++++++++++++++++++
 .../metabolomics-snets-v2/tool.xml            |  2 +-
 3 files changed, 26 insertions(+), 2 deletions(-)

diff --git a/metabolomics-snets-v2/Makefile b/metabolomics-snets-v2/Makefile
index eea9b8df..d516d4af 100644
--- a/metabolomics-snets-v2/Makefile
+++ b/metabolomics-snets-v2/Makefile
@@ -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."
 
diff --git a/metabolomics-snets-v2/metabolomics-snets-v2/input.xml b/metabolomics-snets-v2/metabolomics-snets-v2/input.xml
index 2412824c..d894698c 100644
--- a/metabolomics-snets-v2/metabolomics-snets-v2/input.xml
+++ b/metabolomics-snets-v2/metabolomics-snets-v2/input.xml
@@ -208,6 +208,12 @@
 			<default value="0"/>
 		</parameter>
 
+
+		<parameter name="MAXNETWORKINGPARALLELISM" label="Maxmimum Networking Parallelism">
+			<default value="50"/>
+			<validator type="integer" minimumExclusive="0" maximum="100"/>
+		</parameter>
+
 	</parameters>
 
 
@@ -851,4 +857,22 @@
                             </cell>
 						</row>
 					</block>
+
+					<block label="Advanced Compute Options">
+                        <row>
+							<cell>
+								<label>
+									<content parameter="MAXNETWORKINGPARALLELISM"/>
+								</label>
+							</cell>
+
+							<cell>
+								<input type="text" parameter="MAXNETWORKINGPARALLELISM">
+									<attribute name="size" value="10"/>
+								</input>
+							</cell>
+						</row>
+					</block>
+
+					
 				</interface>
diff --git a/metabolomics-snets-v2/metabolomics-snets-v2/tool.xml b/metabolomics-snets-v2/metabolomics-snets-v2/tool.xml
index 3a5ec9fb..7cd25e74 100644
--- a/metabolomics-snets-v2/metabolomics-snets-v2/tool.xml
+++ b/metabolomics-snets-v2/metabolomics-snets-v2/tool.xml
@@ -100,7 +100,7 @@
             <arg valueRef="mgf_file"/>
             <arg valueRef="workflowParameters"/>
             <arg valueRef="networking_parameters"/>
-            <arg option="-parallelism" value="100"/>
+            <arg option="-parallelism" value="@MAXNETWORKINGPARALLELISM"/>
         </execution>
     </tool>
 

From 32c6957a0e91cfb26d465970a30945f671c28f26 Mon Sep 17 00:00:00 2001
From: Mingxun Wang <mwang87@gmail.com>
Date: Tue, 29 Jun 2021 10:32:33 -0700
Subject: [PATCH 2/2] updating

---
 metabolomics-snets-v2/metabolomics-snets-v2/tool.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/metabolomics-snets-v2/metabolomics-snets-v2/tool.xml b/metabolomics-snets-v2/metabolomics-snets-v2/tool.xml
index 7cd25e74..d3fa7fa6 100644
--- a/metabolomics-snets-v2/metabolomics-snets-v2/tool.xml
+++ b/metabolomics-snets-v2/metabolomics-snets-v2/tool.xml
@@ -100,7 +100,7 @@
             <arg valueRef="mgf_file"/>
             <arg valueRef="workflowParameters"/>
             <arg valueRef="networking_parameters"/>
-            <arg option="-parallelism" value="@MAXNETWORKINGPARALLELISM"/>
+            <arg option="-parallelism" valueRef="@MAXNETWORKINGPARALLELISM"/>
         </execution>
     </tool>