xcms - biotools, edam

workflow4metabolomics · Jan 21, 2020 · 1e674ea · 1e674ea
1 parent cecd1db
commit 1e674ea
Show file tree

Hide file tree

Showing 9 changed files with 63 additions and 0 deletions.
diff --git a/tools/xcms_export_samplemetadata/xcms_export_samplemetadata.xml b/tools/xcms_export_samplemetadata/xcms_export_samplemetadata.xml
@@ -128,4 +128,10 @@ Changelog/News
     ]]></help>
 
     <expand macro="citation" />
+
+    <expand macro="edam_topics"/>
+    <edam_operations>
+        <edam_operation>operation_2409</edam_operation> <!-- Data handling -->
+    </edam_operations>
+    <expand macro="xrefs"/>
 </tool>
diff --git a/tools/xcms_fillpeaks/abims_xcms_fillPeaks.xml b/tools/xcms_fillpeaks/abims_xcms_fillPeaks.xml
@@ -305,5 +305,11 @@ Changelog/News
 
     <expand macro="citation" />
 
+    <expand macro="edam_topics"/>
+    <edam_operations>
+        <edam_operation>operation_3557</edam_operation> <!-- Imputation -->
+    </edam_operations>
+    <expand macro="xrefs"/>
+
 
 </tool>
diff --git a/tools/xcms_group/abims_xcms_group.xml b/tools/xcms_group/abims_xcms_group.xml
@@ -425,5 +425,13 @@ Changelog/News
 
     <expand macro="citation" />
 
+    <expand macro="edam_topics"/>
+    <edam_operations>
+        <edam_operation>operation_3628</edam_operation> <!-- Chromatographic alignment -->
+        <edam_operation>operation_3633</edam_operation> <!-- Retention time prediction -->
+        <edam_operation>operation_3694</edam_operation> <!-- Mass spectrum visualisation -->
+    </edam_operations>
+    <expand macro="xrefs"/>
+
 
 </tool>
diff --git a/tools/xcms_macro/macros_xcms.xml b/tools/xcms_macro/macros_xcms.xml
@@ -252,4 +252,17 @@ For details and explanations concerning all the parameters and workflow of xcms_
             <expand macro="citation_w4m"/>
         </citations>
     </xml>
+    <xml name="edam_topics">
+        <edam_topics>
+            <edam_topic>topic_2259</edam_topic> <!-- Systems biology -->
+            <edam_topic>topic_3172</edam_topic> <!-- Metabolomics -->
+            <edam_topic>topic_3307</edam_topic> <!-- Computational biology -->
+        </edam_topics>
+    </xml>
+    <xml name="xrefs">
+      <xrefs>
+          <xref type="bio.tools">camera</xref>
+          <xref type="bio.tools">workflow4metabolomics</xref>
+      </xrefs>
+    </xml>
 </macros>
diff --git a/tools/xcms_merge/xcms_merge.xml b/tools/xcms_merge/xcms_merge.xml
@@ -198,4 +198,10 @@ Changelog/News
     ]]></help>
 
     <expand macro="citation" />
+
+    <expand macro="edam_topics"/>
+    <edam_operations>
+        <edam_operation>operation_3436</edam_operation> <!-- Aggregation -->
+    </edam_operations>
+    <expand macro="xrefs"/>
 </tool>
diff --git a/tools/xcms_plot_chromatogram/xcms_plot_chromatogram.xml b/tools/xcms_plot_chromatogram/xcms_plot_chromatogram.xml
@@ -116,4 +116,10 @@ Changelog/News
     ]]></help>
 
     <expand macro="citation" />
+
+    <expand macro="edam_topics"/>
+    <edam_operations>
+        <edam_operation>operation_3203</edam_operation> <!-- Chromatogram visualisation -->
+    </edam_operations>
+    <expand macro="xrefs"/>
 </tool>
diff --git a/tools/xcms_retcor/abims_xcms_retcor.xml b/tools/xcms_retcor/abims_xcms_retcor.xml
@@ -375,4 +375,11 @@ Changelog/News
 
     <expand macro="citation" />
 
+    <expand macro="edam_topics"/>
+    <edam_operations>
+        <edam_operation>operation_3628</edam_operation> <!-- Chromatographic alignment -->
+        <edam_operation>operation_3633</edam_operation> <!-- Retention time prediction -->
+    </edam_operations>
+    <expand macro="xrefs"/>
+
 </tool>
diff --git a/tools/xcms_summary/abims_xcms_summary.xml b/tools/xcms_summary/abims_xcms_summary.xml
@@ -129,4 +129,8 @@ Changelog/News
 
     <expand macro="citation" />
 
+    <expand macro="edam_topics"/>
+    <expand macro="edam_operations"/>
+    <expand macro="xrefs"/>
+
 </tool>
diff --git a/tools/xcms_xcmsset/abims_xcms_xcmsSet.xml b/tools/xcms_xcmsset/abims_xcms_xcmsSet.xml
@@ -581,4 +581,11 @@ Changelog/News
     ]]></help>
 
     <expand macro="citation" />
+
+    <expand macro="edam_topics"/>
+    <edam_operations>
+        <edam_operation>operation_3215</edam_operation> <!-- Peak detection -->
+        <edam_operation>operation_3860</edam_operation> <!-- Spectrum calculation -->
+    </edam_operations>
+    <expand macro="xrefs"/>
 </tool>