comparison raceid_trajectory.xml @ 8:c92d0f9338c5 draft

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

7:e93b008c637a

<tool id="raceid_trajectory" name="Lineage computation using StemID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
    <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="rdata" label="Input RDS" help="This is the output RData 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." />

        </section>
        <param name="use_log" type="boolean" checked="false" label="Output Log?" />
    </inputs>
    <outputs>
        <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
        <data name="outrdat" format="rdata" label="${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>

8:c92d0f9338c5

<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." />

        </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>