annotate raceid_trajectory.xml @ 8:c92d0f9338c5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 455bad7eca54164f95755174904842907846bb42"

<tool id="raceid_trajectory" name="Lineage computation using StemID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>generates lineage from prior clustering</description>
    <macros>
        <import>macros.xml</import>
        <import>macros_cheetah.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command_config" prog="pseudotemporal.R" cheetah="TRAJECTORY_CHEETAH" />

    <inputs>
        <param name="inputrds" type="data" format="rds" label="Input RDS" help="This is the output RDS file given by the Cluster stage" />
        <section name="projcell" title="Compute transcriptome entropy of each cell" expanded="true" >
            <param name="knn" type="integer" min="0" value="3" label="KNN" help="Number of nearest neighbours to consider." />
            <param name="cthr" type="integer" min="0" value="5" label="Cluster Threshold" help="Clusters to be included in the StemID analysis must have more than this number of cells" />
            <expand macro="use_defaults_no" >
                <param name="nmode" type="boolean" checked="true" label="Neighbour Mode" help="Assign a cell of a given cluster to the cluster with the smallest average distance of the knn nearest neighbours within this cluster." />
                <param name="fr" type="boolean" checked="false" label="F-R layout?" help="Use Fruchterman-Rheigold layout instead of t-SNE" />
            </expand>
        </section>
        <section name="projback" title="Compute Cell Projections for Randomized Background Distribution" expanded="true" >
            <param name="pdishuf" type="integer" min="100" value="2000" label="Shuffle Projections" help="Number of randomizations of cell positions for which to compute projections of cells on inter-cluster links" />
            <expand macro="use_defaults_no" >
                <param name="fast" type="boolean" checked="false" label="Use a fast approximate background model to infer links" />
                <param name="rseed" type="integer" value="17000" label="Random seed" />
            </expand>
        </section>
        <section name="comppval" title="Computing P-values for Link Significance" expanded="true" >
            <param name="pthr" type="float" value="0.01" label="P-value cutoff" help="Cutoff for link significance. This threshold is applied for the calculation of link scores reflecting how uniformly a link is occupied by cells." />
            <param name="sensitive" type="boolean" checked="false" label="Sensitivity" help="All cells on the most highly significant link are and the link itself are disregard to test significance of the remaining links with a binomial p-value" />
        </section>
        <section name="plotgraph" title="StemID2 Lineage Graph" expanded="true" >
            <param name="showcells" type="boolean" checked="false" label="Show Cells" help="Projections of cells are shown in the plot" />
            <param name="scthr" type="float" min="0" max="1" value="0" label="Score Threshold" help="Score threshold for links to be shown in the graph" />
            <expand macro="use_defaults_no">
                <!-- <param name="showtsne" type="boolean" checked="true" label="Show tSNE" help="Show transparent t-SNE map of cells in the background" /> -->
                <param name="tp" type="float" min="0" max="1" value="0.5" label="Transparency" help="Level of transparency of t-SNE map" />
            </expand>
        </section>
        <section name="compscore" title="Compute StemID2 score" expanded="true" >
            <param name="nn" type="integer" min="0" value="1" label="Number of Neighbours" help="Number of higher order neighbours to be included for the determination of links" />
            <param name="scthr" type="float" min="0" max="1" value="0" label="Score Threshold" help="Score threshold for links to be included in the calculation" />
        </section>
        <param name="use_log" type="boolean" checked="false" label="Output Log?" />
    </inputs>
    <outputs>
        <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
        <data name="outrdat" format="rds" label="${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>
        <test>
            <!-- All defaults -->
            <param name="inputrds" value="out_cluster_default.rdat" />
            <output name="outpdf" value="out_traject_default.pdf" compare="sim_size" delta="15" />
            <output name="outrdat" value="out_traject_default.ltree.rdat" compare="sim_size" delta="500" />
        </test>
        <test>
            <!-- Manually specify the defaults: should ideally give same output as above test -->
            <param name="inputrds" value="out_cluster_default.rdat" />
            <section name="projcell" >
                <param name="knn" value="3" />
                <param name="cthr" value="5" />
                <expand macro="test_nondef" >
                    <param name="nmode" value="true" />
                    <param name="fr" value="false" />
                </expand>
            </section>
            <section name="projback" >
                <param name="pdishuf" value="2000" />
                <expand macro="test_nondef" >
                    <param name="fast" value="false" />
                    <param name="rseed" value="17000" />
                </expand>
            </section>
            <section name="comppval" >
                <param name="pthr" value="0.01" />
                <param name="sensitive" value="false" />
            </section>
            <section name="plotgraph" >
                <param name="showcells" value="false" />
                <param name="scthr" value="0" />
                <expand macro="test_nondef" >
                    <!-- <param name="showtsne" value="true" /> -->
                    <param name="tp" value="0.5" />
                </expand>
            </section>
            <section name="compscore" >
                <param name="nn" value="1" />
                <param name="scthr" value="0" />
            </section>
            <output name="outpdf" value="out_traject_default.pdf" compare="sim_size" delta="500" />
            <output name="outrdat" value="out_traject_default.ltree.rdat" compare="sim_size" delta="500" />
        </test>
        <test>
            <!-- Non-defaults -->
            <param name="inputrds" value="out_cluster_default.rdat" />
            <section name="projcell">
                <param name="knn" value="4" />
                <param name="cthr" value="4" />
                <expand macro="test_nondef" >
                    <param name="nmode" value="false" />
                    <param name="fr" value="true" />
                </expand>
            </section>
            <section name="projback">
                <param name="pdishuf" value="1500" />
                <expand macro="test_nondef" >
                    <param name="fast" value="true" />
                    <param name="rseed" value="1500" />
                </expand>
            </section>
            <section name="comppval">
                <param name="pthr" value="0.05" />
                <param name="sensitive" value="true" />
            </section>
            <section name="plotgraph">
                <param name="showcells" value="true" />
                <param name="scthr" value="0.5" />
                <expand macro="test_nondef" >
               <!--     <param name="showtsne" value="false" /> -->
                    <param name="tp" value="0.25" />
                </expand>
            </section>
            <section name="compscore">
                <param name="nn" value="2" />
                <param name="scthr" value="0.5" />
            </section>
            <output name="outpdf" value="out_traject_adv_nondef.pdf" compare="sim_size" delta="500" />
        </test>
    </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>