<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>