From 43c7c8e899bb70d4575e21c27b160b56fee42544 Mon Sep 17 00:00:00 2001
From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com>
Date: Tue, 5 Nov 2024 17:38:50 +0100
Subject: [PATCH] swap xrefs and requirements

---
 tools/tertiary-analysis/garnett/garnett_macros.xml   | 10 +++++-----
 tools/tertiary-analysis/monocle3/monocle3-macros.xml | 12 ++++++------
 tools/tertiary-analysis/pyscenic/macros.xml          | 10 +++++-----
 tools/tertiary-analysis/sc3/sc3-macros.xml           | 10 +++++-----
 tools/tertiary-analysis/scater/scater_macros.xml     | 10 +++++-----
 tools/tertiary-analysis/sceasy/sceasy_macros.xml     | 11 ++++++-----
 tools/tertiary-analysis/scmap/scmap_macros.xml       | 10 +++++-----
 tools/tertiary-analysis/scpred/scpred_macros.xml     | 10 +++++-----
 8 files changed, 42 insertions(+), 41 deletions(-)

diff --git a/tools/tertiary-analysis/garnett/garnett_macros.xml b/tools/tertiary-analysis/garnett/garnett_macros.xml
index 8821fd1a..c5c7508d 100644
--- a/tools/tertiary-analysis/garnett/garnett_macros.xml
+++ b/tools/tertiary-analysis/garnett/garnett_macros.xml
@@ -2,17 +2,17 @@
     <token name="@TOOL_VERSION@">0.2.8</token>
     <token name="@HELP@">More information can be found at https://cole-trapnell-lab.github.io/garnett/docs/</token>
     <token name="@PROFILE@">18.01</token>
+    <xml name="xrefs">
+      <xrefs>
+          <xref type="bio.tools">Garnett</xref>
+      </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="0.0.5">garnett-cli</requirement>
             <yield/>
         </requirements>
     </xml>
-    <xml name="xrefs">
-      <xrefs>
-          <xref type="bio.tools">Garnett</xref>
-      </xrefs>
-    </xml>
     <xml name="version">
         <version_command><![CDATA[
         echo $(R --version | grep version | grep -v GNU)", garnett version" $(R --vanilla --slave -e "library(garnett); cat(sessionInfo()\$otherPkgs\$garnett\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
diff --git a/tools/tertiary-analysis/monocle3/monocle3-macros.xml b/tools/tertiary-analysis/monocle3/monocle3-macros.xml
index 2dda551d..a6d4a837 100644
--- a/tools/tertiary-analysis/monocle3/monocle3-macros.xml
+++ b/tools/tertiary-analysis/monocle3/monocle3-macros.xml
@@ -29,6 +29,12 @@
 #end if
   </token>
 
+  <xml name="xrefs">
+    <xrefs>
+      <xref type="bio.tools">monocle</xref>
+    </xrefs>
+  </xml>
+
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="0.0.7">monocle3-cli</requirement>
@@ -36,12 +42,6 @@
     </requirements>
   </xml>
 
-  <xml name="xrefs">
-    <xrefs>
-      <xref type="bio.tools">monocle</xref>
-    </xrefs>
-  </xml>
-
   <xml name="citations">
     <citations>
       <yield />
diff --git a/tools/tertiary-analysis/pyscenic/macros.xml b/tools/tertiary-analysis/pyscenic/macros.xml
index 18a2bc63..921e3bea 100644
--- a/tools/tertiary-analysis/pyscenic/macros.xml
+++ b/tools/tertiary-analysis/pyscenic/macros.xml
@@ -1,5 +1,10 @@
 <macros>
     <token name="@TOOL_VERSION@">0.12.1</token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">maaslin2</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
             <container type="docker">
@@ -7,11 +12,6 @@
         </container>
         </requirements>
     </xml>
-    <xml name="xrefs">
-        <xrefs>
-            <xref type="bio.tools">maaslin2</xref>
-        </xrefs>
-    </xml>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1038/nmeth.4463</citation>
diff --git a/tools/tertiary-analysis/sc3/sc3-macros.xml b/tools/tertiary-analysis/sc3/sc3-macros.xml
index 86bff088..3a64dc6c 100644
--- a/tools/tertiary-analysis/sc3/sc3-macros.xml
+++ b/tools/tertiary-analysis/sc3/sc3-macros.xml
@@ -1,17 +1,17 @@
 <macros>
   <token name="@TOOL_VERSION@">1.8.0</token>
   <token name="@HELP@">Documentation can be found at http://bioconductor.org/packages/release/bioc/vignettes/SC3/inst/doc/SC3.html</token>
+  <xml name="xrefs">
+      <xrefs>
+          <xref type="bio.tools">sc3</xref>
+      </xrefs>
+  </xml>
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="0.0.4">sc3-scripts</requirement>
       <yield/>
     </requirements>
   </xml>
-  <xml name="xrefs">
-      <xrefs>
-          <xref type="bio.tools">sc3</xref>
-      </xrefs>
-  </xml>
   <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
 
diff --git a/tools/tertiary-analysis/scater/scater_macros.xml b/tools/tertiary-analysis/scater/scater_macros.xml
index e096b1cb..263bf130 100644
--- a/tools/tertiary-analysis/scater/scater_macros.xml
+++ b/tools/tertiary-analysis/scater/scater_macros.xml
@@ -1,17 +1,17 @@
 <macros>
   <token name="@TOOL_VERSION@">1.10.0</token>
   <token name="@HELP@">More information can be found at https://bioconductor.org/packages/release/bioc/html/scater.html</token>
-  <xml name="requirements">
-    <requirements>
-      <requirement type="package" version="0.0.5">scater-scripts</requirement>
-      <yield/>
-    </requirements>
   </xml>
   <xml name="xrefs">
     <xrefs>
       <xref type="bio.tools">scater</xref>
     </xrefs>
   </xml>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="0.0.5">scater-scripts</requirement>
+      <yield/>
+    </requirements>
   <xml name="version">
     <version_command><![CDATA[
     echo $(R --version | grep version | grep -v GNU)", scater version" $(R --vanilla --slave -e "library(scater); cat(sessionInfo()\$otherPkgs\$scater\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
diff --git a/tools/tertiary-analysis/sceasy/sceasy_macros.xml b/tools/tertiary-analysis/sceasy/sceasy_macros.xml
index 8ad68886..a1e126d1 100644
--- a/tools/tertiary-analysis/sceasy/sceasy_macros.xml
+++ b/tools/tertiary-analysis/sceasy/sceasy_macros.xml
@@ -7,17 +7,18 @@
 0.0.1+galaxy0: Initial version based on sceasy 0.0.5 by Ni Huang, WTSI.
     ]]></token>
 
+  <xml name="xrefs">
+    <xrefs>
+      <xref type="bio.tools">sceasy</xref>
+    </xrefs>
+  </xml>
+
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="0.0.5">r-sceasy</requirement>
       <yield/>
     </requirements>
   </xml>
-  <xml name="xrefs">
-    <xrefs>
-      <xref type="bio.tools">sceasy</xref>
-    </xrefs>
-  </xml>
 
   <xml name="citations">
     <citations>
diff --git a/tools/tertiary-analysis/scmap/scmap_macros.xml b/tools/tertiary-analysis/scmap/scmap_macros.xml
index 8ac391c8..0a3ec398 100644
--- a/tools/tertiary-analysis/scmap/scmap_macros.xml
+++ b/tools/tertiary-analysis/scmap/scmap_macros.xml
@@ -2,6 +2,11 @@
     <token name="@TOOL_VERSION@">1.6.4</token>
     <token name="@HELP@">More information can be found at https://bioconductor.org/packages/release/bioc/html/scmap.html</token>
     <token name="@PROFILE@">18.01</token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">scmap</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
       <requirements>
         <requirement type="package" version="0.1.0">scmap-cli</requirement>
@@ -21,11 +26,6 @@
 1.6.1+galaxy0: Update scmap-cli to 0.0.9.
 1.6.0+galaxy0: Initial contribution. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
     ]]></token>
-    <xml name="xrefs">
-        <xrefs>
-            <xref type="bio.tools">scmap</xref>
-        </xrefs>
-      </xml>
     <xml name="citations">
       <citations>
         <citation type="bibtex">
diff --git a/tools/tertiary-analysis/scpred/scpred_macros.xml b/tools/tertiary-analysis/scpred/scpred_macros.xml
index ccf17101..99788754 100644
--- a/tools/tertiary-analysis/scpred/scpred_macros.xml
+++ b/tools/tertiary-analysis/scpred/scpred_macros.xml
@@ -2,6 +2,11 @@
     <token name="@TOOL_VERSION@">1.0.2</token>
     <token name="@HELP@">More information can be found at https://joseah.github.io/post/introduction-to-scpred/</token>
     <token name="@PROFILE@">18.01</token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">scPred</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="0.1.0">scpred-cli</requirement>
@@ -19,11 +24,6 @@
         1.0.1+galaxy0: Update output format from csv to tsv
         1.0.0+galaxy0: Initilal contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
         ]]></token>
-    <xml name="xrefs">
-        <xrefs>
-            <xref type="bio.tools">scPred</xref>
-        </xrefs>
-    </xml>
     <xml name="citations">
         <citations>
             <citation type="bibtex">