From 38cb46bf34ebd2ceb18fd24d7eed374b89a68503 Mon Sep 17 00:00:00 2001
From: Pavankumar Videm <pavanvidem@gmail.com>
Date: Tue, 5 Nov 2024 15:03:56 +0100
Subject: [PATCH] RaceID link newly created bio.tools entry

---
 tools/raceid/macros.xml                     | 5 +++++
 tools/raceid/raceid_clustering.xml          | 1 +
 tools/raceid/raceid_filtnormconf.xml        | 1 +
 tools/raceid/raceid_inspectclusters.xml     | 1 +
 tools/raceid/raceid_inspecttrajectories.xml | 1 +
 tools/raceid/raceid_trajectory.xml          | 3 ++-
 6 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/tools/raceid/macros.xml b/tools/raceid/macros.xml
index 94b7bf81a83..2a8ccc46f1d 100644
--- a/tools/raceid/macros.xml
+++ b/tools/raceid/macros.xml
@@ -52,6 +52,11 @@ Rscript '$__tool_directory__/scripts/@PROG@' '$userconf' @OUT@
             <!-- <requirement type="package" version="1.6.2">bioconductor-scran</requirement> -->
         </requirements>
     </macro>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">RaceID</xref>
+        </xrefs>
+      </xml>
     <macro name="yesno_checkedno" >
         <option value="yes" >Yes</option>
         <option value="no" selected="true" >No</option>
diff --git a/tools/raceid/raceid_clustering.xml b/tools/raceid/raceid_clustering.xml
index 39fb1c5e555..efc47bea70f 100644
--- a/tools/raceid/raceid_clustering.xml
+++ b/tools/raceid/raceid_clustering.xml
@@ -4,6 +4,7 @@
         <import>macros.xml</import>
         <import>macros_cheetah.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="version_command_config" prog="cluster.R" cheetah="CLUSTER_CHEETAH" out="&#38;&#62; '$outlog'" />
 
diff --git a/tools/raceid/raceid_filtnormconf.xml b/tools/raceid/raceid_filtnormconf.xml
index 4299719aaaa..6499841e6e2 100644
--- a/tools/raceid/raceid_filtnormconf.xml
+++ b/tools/raceid/raceid_filtnormconf.xml
@@ -4,6 +4,7 @@
         <import>macros.xml</import>
         <import>macros_cheetah.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="version_command_config" prog="cluster.R" cheetah="FILTNORM_CHEETAH" out="2&#62; '$outlog' &#62; /dev/null" />
     <inputs>
diff --git a/tools/raceid/raceid_inspectclusters.xml b/tools/raceid/raceid_inspectclusters.xml
index 7dfcbf2e79c..acc2e767eec 100644
--- a/tools/raceid/raceid_inspectclusters.xml
+++ b/tools/raceid/raceid_inspectclusters.xml
@@ -34,6 +34,7 @@
             </section>
         </macro>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="version_command_config" prog="clusterinspect.R" cheetah="INSPECTCLUSTERS_CHEETAH" out="&#38;&#62; '$outlog'" />
     <inputs>
diff --git a/tools/raceid/raceid_inspecttrajectories.xml b/tools/raceid/raceid_inspecttrajectories.xml
index 5a0e1437d1d..d62387fd9cd 100644
--- a/tools/raceid/raceid_inspecttrajectories.xml
+++ b/tools/raceid/raceid_inspecttrajectories.xml
@@ -4,6 +4,7 @@
         <import>macros.xml</import>
         <import>macros_cheetah.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="version_command_config" prog="trajectoryinspect.R" cheetah="INSPECTTRAJECTORIES_CHEETAH" />
     <inputs>
diff --git a/tools/raceid/raceid_trajectory.xml b/tools/raceid/raceid_trajectory.xml
index 536790f8ebc..6fcaf710b67 100644
--- a/tools/raceid/raceid_trajectory.xml
+++ b/tools/raceid/raceid_trajectory.xml
@@ -4,6 +4,7 @@
         <import>macros.xml</import>
         <import>macros_cheetah.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="version_command_config" prog="pseudotemporal.R" cheetah="TRAJECTORY_CHEETAH" />
 
@@ -136,7 +137,7 @@ StemID2
 
 StemID is an algorithm for the inference of lineage trees and differentiation trajectories based on pseudo-temporal ordering of single-cell transcriptomes. It utilizies the clusters predicted by RaceID clustering tool.
 
-In a nutshell, StemID infers links between clusters which are more populated with intermediate single-cell transcriptomes than expected by chance. 
+In a nutshell, StemID infers links between clusters which are more populated with intermediate single-cell transcriptomes than expected by chance.
 
 This will generate an RDS object, and a PDF showing a minimal spanning tree between the clusters, with the strength between clusters given by the colour and thickness of the branches.