Merge pull request galaxyproject#6532 from pavanvidem/xref-raceid

RaceID link newly created bio.tools entry
pavanvidem · Nov 5, 2024 · 0ffa71e · 0ffa71e
2 parents d1eee78 + 38cb46b
commit 0ffa71e
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Showing 6 changed files with 11 additions and 1 deletion.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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.