annotate raceid_trajectory.xml @ 1:30d9118a650a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 71e6b205841c83391ea8fc69e10eac03f212f4d6

<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>