From 1e674ea124cb1da81945e0f67fd2fc7491c95d85 Mon Sep 17 00:00:00 2001
From: lecorguille <gildas.le.corguille@gmail.com>
Date: Tue, 21 Jan 2020 17:59:20 +0100
Subject: [PATCH] xcms - biotools, edam

---
 .../xcms_export_samplemetadata.xml                  |  6 ++++++
 tools/xcms_fillpeaks/abims_xcms_fillPeaks.xml       |  6 ++++++
 tools/xcms_group/abims_xcms_group.xml               |  8 ++++++++
 tools/xcms_macro/macros_xcms.xml                    | 13 +++++++++++++
 tools/xcms_merge/xcms_merge.xml                     |  6 ++++++
 .../xcms_plot_chromatogram.xml                      |  6 ++++++
 tools/xcms_retcor/abims_xcms_retcor.xml             |  7 +++++++
 tools/xcms_summary/abims_xcms_summary.xml           |  4 ++++
 tools/xcms_xcmsset/abims_xcms_xcmsSet.xml           |  7 +++++++
 9 files changed, 63 insertions(+)

diff --git a/tools/xcms_export_samplemetadata/xcms_export_samplemetadata.xml b/tools/xcms_export_samplemetadata/xcms_export_samplemetadata.xml
index 6f8bb93f33..10b026e500 100644
--- 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
index de086c069e..207058b901 100644
--- 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
index f618e2b912..401536ea99 100644
--- 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
index b0a92e196f..64be46d6ea 100644
--- 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
index aa28cb3495..5f3c9a85d4 100644
--- 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
index 5b032d1113..1da64373b0 100644
--- 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
index 30585ef133..b0e73f7b20 100644
--- 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
index 8c858112d2..d1914fae51 100644
--- 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
index 436784ef79..391d0ec801 100644
--- 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>