From 3ade70ce8c3d73a9cb457bd35fc22a1054396288 Mon Sep 17 00:00:00 2001
From: lecorguille <gildas.le.corguille@gmail.com>
Date: Tue, 21 Jan 2020 15:13:28 +0100
Subject: [PATCH 1/5] camera - biotools, edam

---
 .../abims_CAMERA_annotateDiffreport.xml       |  3 +++
 .../abims_CAMERA_combinexsAnnos.xml           |  4 ++++
 tools/camera_macro/macros.xml                 | 19 +++++++++++++++++++
 3 files changed, 26 insertions(+)

diff --git a/tools/camera_annotate/abims_CAMERA_annotateDiffreport.xml b/tools/camera_annotate/abims_CAMERA_annotateDiffreport.xml
index 86a03b00a5..e6badc4d4f 100644
--- a/tools/camera_annotate/abims_CAMERA_annotateDiffreport.xml
+++ b/tools/camera_annotate/abims_CAMERA_annotateDiffreport.xml
@@ -514,5 +514,8 @@ Changelog/News
 
     <expand macro="citation" />
 
+    <expand macro="edam_topics"/>
+    <expand macro="edam_operations"/>
+    <expand macro="xrefs"/>
 
 </tool>
diff --git a/tools/camera_combinexsannos/abims_CAMERA_combinexsAnnos.xml b/tools/camera_combinexsannos/abims_CAMERA_combinexsAnnos.xml
index 9e6b57c602..400186eda4 100644
--- a/tools/camera_combinexsannos/abims_CAMERA_combinexsAnnos.xml
+++ b/tools/camera_combinexsannos/abims_CAMERA_combinexsAnnos.xml
@@ -263,5 +263,9 @@ Changelog/News
 
     <expand macro="citation" />
 
+    <expand macro="edam_topics"/>
+    <expand macro="edam_operations"/>
+    <expand macro="xrefs"/>
+
 
 </tool>
diff --git a/tools/camera_macro/macros.xml b/tools/camera_macro/macros.xml
index 84e4a5f1ab..fb6a136e2e 100644
--- a/tools/camera_macro/macros.xml
+++ b/tools/camera_macro/macros.xml
@@ -165,4 +165,23 @@
             <citation type="doi">10.1093/bioinformatics/btu813</citation>
         </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="edam_operations">
+      <edam_operations>
+          <edam_operation>operation_0226</edam_operation> <!-- Annotation -->
+          <edam_operation>operation_3501</edam_operation> <!-- Enrichment analysis -->
+      </edam_operations>
+    </xml>
+    <xml name="xrefs">
+      <xrefs>
+          <xref type="bio.tools">camera</xref>
+          <xref type="bio.tools">workflow4metabolomics</xref>
+      </xrefs>
+    </xml>
 </macros>

From 2cd106e7d9bfd4acbebbdd23a3bf35101a74d143 Mon Sep 17 00:00:00 2001
From: lecorguille <gildas.le.corguille@gmail.com>
Date: Tue, 21 Jan 2020 15:23:04 +0100
Subject: [PATCH 2/5] ipo - biotools, edam

---
 tools/ipo/ipo4retgroup.xml |  4 ++++
 tools/ipo/ipo4xcmsSet.xml  |  4 ++++
 tools/ipo/macros.xml       | 20 ++++++++++++++++++++
 3 files changed, 28 insertions(+)

diff --git a/tools/ipo/ipo4retgroup.xml b/tools/ipo/ipo4retgroup.xml
index 2f2e2d706e..85e3ed736b 100644
--- a/tools/ipo/ipo4retgroup.xml
+++ b/tools/ipo/ipo4retgroup.xml
@@ -229,4 +229,8 @@ Changelog/News
     ]]></help>
 
     <expand macro="citation" />
+
+    <expand macro="edam_topics"/>
+    <expand macro="edam_operations"/>
+    <expand macro="xrefs"/>
 </tool>
diff --git a/tools/ipo/ipo4xcmsSet.xml b/tools/ipo/ipo4xcmsSet.xml
index 769bf3df82..e2dab48fee 100644
--- a/tools/ipo/ipo4xcmsSet.xml
+++ b/tools/ipo/ipo4xcmsSet.xml
@@ -252,4 +252,8 @@ Changelog/News
     ]]></help>
 
     <expand macro="citation" />
+
+    <expand macro="edam_topics"/>
+    <expand macro="edam_operations"/>
+    <expand macro="xrefs"/>
 </tool>
diff --git a/tools/ipo/macros.xml b/tools/ipo/macros.xml
index d2dcd27f5b..394a6ea347 100644
--- a/tools/ipo/macros.xml
+++ b/tools/ipo/macros.xml
@@ -89,4 +89,24 @@
             <citation type="doi">10.1093/bioinformatics/btu813</citation>
         </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="edam_operations">
+      <edam_operations>
+          <edam_operation>operation_3627</edam_operation> <!-- Mass spectra calibration -->
+          <edam_operation>operation_3215</edam_operation> <!-- Peak detection -->
+          <edam_operation>operation_2425</edam_operation> <!-- Optimisation and refinement -->
+      </edam_operations>
+    </xml>
+    <xml name="xrefs">
+      <xrefs>
+          <xref type="bio.tools">ipo</xref>
+          <xref type="bio.tools">workflow4metabolomics</xref>
+      </xrefs>
+    </xml>
 </macros>

From a667971bfd1148954aab5b71236a1c4be241a6a6 Mon Sep 17 00:00:00 2001
From: lecorguille <gildas.le.corguille@gmail.com>
Date: Tue, 21 Jan 2020 16:08:20 +0100
Subject: [PATCH 3/5] msnbase - biotools, edam

---
 .../msnbase_readmsdata/msnbase_readmsdata.xml |  4 ++++
 tools/xcms_macro/macros_msnbase.xml           | 20 +++++++++++++++++++
 2 files changed, 24 insertions(+)

diff --git a/tools/msnbase_readmsdata/msnbase_readmsdata.xml b/tools/msnbase_readmsdata/msnbase_readmsdata.xml
index 4bc1f82b73..0e27fdba81 100644
--- a/tools/msnbase_readmsdata/msnbase_readmsdata.xml
+++ b/tools/msnbase_readmsdata/msnbase_readmsdata.xml
@@ -251,4 +251,8 @@ Changelog/News
     ]]></help>
 
     <expand macro="citation" />
+
+    <expand macro="edam_topics"/>
+    <expand macro="edam_operations"/>
+    <expand macro="xrefs"/>
 </tool>
diff --git a/tools/xcms_macro/macros_msnbase.xml b/tools/xcms_macro/macros_msnbase.xml
index a1a1c39b8d..1869baa439 100644
--- a/tools/xcms_macro/macros_msnbase.xml
+++ b/tools/xcms_macro/macros_msnbase.xml
@@ -28,4 +28,24 @@
             <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_0121</edam_topic> <!-- Proteomics -->
+            <edam_topic>topic_3307</edam_topic> <!-- Computational biology -->
+        </edam_topics>
+    </xml>
+    <xml name="edam_operations">
+      <edam_operations>
+          <edam_operation>operation_2409</edam_operation> <!-- Data handling -->
+      </edam_operations>
+    </xml>
+    <xml name="xrefs">
+      <xrefs>
+          <xref type="bio.tools">msnbase</xref>
+          <xref type="bio.tools">workflow4metabolomics</xref>
+      </xrefs>
+    </xml>
 </macros>

From cecd1db8c1daad84b6657d38b0615d4a3c8affbc Mon Sep 17 00:00:00 2001
From: lecorguille <gildas.le.corguille@gmail.com>
Date: Tue, 21 Jan 2020 16:12:20 +0100
Subject: [PATCH 4/5] asics - biotools, edam

---
 tools/nmr_annotation/asics_xml.xml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/tools/nmr_annotation/asics_xml.xml b/tools/nmr_annotation/asics_xml.xml
index c044f5f873..69736d44cf 100644
--- a/tools/nmr_annotation/asics_xml.xml
+++ b/tools/nmr_annotation/asics_xml.xml
@@ -222,5 +222,17 @@ Example
        <citation type="doi">10.1007/s11306-017-1244-5</citation>
        <citation type="doi">10.1093/bioinformatics/btu813</citation>
    </citations>
+   <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>
+   <edam_operations>
+       <edam_operation>operation_0226</edam_operation> <!-- Annotation -->
+   </edam_operations>
+   <xrefs>
+       <xref type="bio.tools">asics</xref>
+       <xref type="bio.tools">workflow4metabolomics</xref>
+   </xrefs>
 
 </tool>

From c6b57ad9586d5fb349520ff3c6574f4067b2b40d 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 5/5] 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           |  5 +++++
 tools/xcms_xcmsset/abims_xcms_xcmsSet.xml           |  7 +++++++
 9 files changed, 64 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..ef07a26732 100644
--- a/tools/xcms_summary/abims_xcms_summary.xml
+++ b/tools/xcms_summary/abims_xcms_summary.xml
@@ -128,5 +128,10 @@ Changelog/News
 
 
     <expand macro="citation" />
+    <edam_operations>
+        <edam_operation>operation_0337</edam_operation> <!-- Visualisation -->
+    </edam_operations>
+    <expand macro="edam_topics"/>
+    <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>