Mercurial > repos > iuc > raceid_trajectory
diff raceid_trajectory.xml @ 0:ff7cd3c7c1df draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
author | iuc |
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date | Thu, 22 Nov 2018 04:43:00 -0500 |
parents | |
children | 3e5bb16abb55 |
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--- /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> +