diff raceid_inspecttrajectories.xml @ 0:e0e9b24d76aa 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_inspecttrajectories.xml	Thu Nov 22 04:42:18 2018 -0500
@@ -0,0 +1,57 @@
+<tool id="raceid_inspecttrajectory" name="Lineage Branch Analysis using StemID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.1" >
+    <description>inspects branches of a lineage tree</description>
+    <macros>
+        <import>macros.xml</import>
+        <import>macros_inspecttrajectories.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <version_command><![CDATA[
+Rscript '$__tool_directory__/scripts/trajectoryinspect.R' @GET_VERSION@
+]]></version_command>
+
+    <command detect_errors="exit_code"><![CDATA[
+#set bin = 'trajectoryinspect.R'
+Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2>&1 > '$outlog'
+    ]]></command>
+  
+    <configfiles>
+        <configfile name="userconf" ><![CDATA[
+@STRING2VECTOR@
+
+@INSPECTTRAJECTORIES_CHEETAH@
+]]>
+        </configfile>
+    </configfiles>
+
+    <inputs>
+        <expand macro="inspecttrajectories_inputs" />
+    </inputs>
+
+    <outputs>
+        <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
+        <data name="outdiffgenes" format="tabular" label="${tool.name} on ${on_string}: TrajectoryInspect - Differential Genes" >
+            <filter>trjsid['basic']['doit'] == "yes"</filter>
+        </data>
+        <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" >
+            <filter>use_log</filter>
+        </data>
+
+    </outputs>
+    <tests>
+        <expand macro="inspecttrajectories_tests" />
+    </tests>
+    <help><![CDATA[
+StemID2 and FateID
+=====================
+
+Given a previous lineage tree generated an RDS file generated from the previous Trajectory step, we can explore the variation of gene expression for all cells that lie on a given branch or trajectory.
+
+This will generate a PDF containing a heatmap of expression for all neighboring clusters that share links with  cluster 5, as well as a plot of all cells along the branches between 1 to 3 and 3 to 10. A table of the most differentially expressed genes across these projection will also be output, which will provide a more qualitative assessment of how signficant our Apoa-expressing genes are along this projection.
+
+For more information on the different types cluster and trajectory inspection that can be performed, please consult the RaceID vignette_.
+
+.. _vignette: https://github.com/dgrun/RaceID3_StemID2_package/blob/master/vignettes/RaceID.Rmd
+
+]]></help>
+    <expand macro="citations" />
+</tool>