Mercurial > repos > iuc > raceid_trajectory
view raceid_trajectory.xml @ 2:87de515af823 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 1d6e79ba92ce98c7c91f0c4076c9ca5e4e3f3a20
author | iuc |
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date | Thu, 28 Feb 2019 17:39:28 -0500 |
parents | ff7cd3c7c1df |
children | 3e5bb16abb55 |
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<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>