diff raceid_trajectory.xml @ 0:ff7cd3c7c1df draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/raceid_trajectory.xml	Thu Nov 22 04:43:00 2018 -0500
@@ -0,0 +1,53 @@
+<tool id="raceid_trajectory" name="Lineage computation using StemID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.1" >
+    <description>generates lineage from prior clustering</description>
+    <macros>
+        <import>macros.xml</import>
+        <import>macros_trajectory.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <version_command><![CDATA[
+Rscript '$__tool_directory__/scripts/pseudotemporal.R' @GET_VERSION@
+]]></version_command>
+
+    <command detect_errors="exit_code"><![CDATA[
+#set bin = 'pseudotemporal.R'
+Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2>&1 > '$outlog'
+    ]]></command>
+  
+    <configfiles>
+        <configfile name="userconf" ><![CDATA[
+@STRING2VECTOR@
+
+@TRAJECTORY_CHEETAH@
+]]>
+        </configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="trajectory_inputs" />
+        <param name="use_log" type="boolean" checked="false" label="Output Log?" />
+    </inputs>
+    <outputs>
+        <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
+        <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" />
+        <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" >
+            <filter>use_log</filter>
+        </data>
+    </outputs>
+    <tests>
+        <expand macro="trajectory_tests" />
+    </tests>
+    <help><![CDATA[
+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. 
+
+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.
+
+
+]]></help>
+    <expand macro="citations" />
+</tool>
+