comparison raceid_clustering.xml @ 7:c4f39bf4a068 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit b461ba94158cf4cc793919470b78bd3eb91312eb"

6:a4b734cd253b

<tool id="raceid_clustering" name="Clustering using RaceID" version="@VERSION_RACEID@+galaxy@VERSION_WRAPPER@" >
    <description>performs clustering, outlier detection, dimensional reduction</description>
    <macros>
        <import>macros.xml</import>
        <import>macros_cheetah.xml</import>
    </macros>

                <param name="probthr" type="float" min="0" value="0.001" label="Outlier Probability Threshold" help="Probability threshold for the above specified minimum number of genes to be an outlier cell. This probability is computed from a negative binomial background model of expression in a cluster" />
                <param name="outdistquant" type="float" min="0" max="1" value="0.95" label="Outlier Distance Quantile" help="Outlier cells are merged to outlier clusters if their distance smaller than the outdistquant-quantile of the distance distribution of pairs of cells in the orginal clusters after outlier removal" />
                <!-- RFCorrect -->
                <param name="nbtree" type="integer" optional="true" label="Number of trees to be built" /><!-- 0:Null -->
                <param name="nbfactor" type="integer" min="0" value="5" label="Tree Factor" help="Number of trees based on the number of cells multiplied by this factor. Effective only if the number of trees parameter is set to 0" />
                <param name="rfseed" type="integer" value="12345" label="Random Seed" />
            </expand>
        </section>
        <section name="tsne" title="tSNE, FR and UMAP" expanded="true" >
            <!-- CompTSNE -->
            <param name="perplexity" type="integer" min="0" value="30" label="Perplexity" help="Perplexity of the t-SNE map" />

7:c4f39bf4a068

<tool id="raceid_clustering" name="Clustering using RaceID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
    <description>performs clustering, outlier detection, dimensional reduction</description>
    <macros>
        <import>macros.xml</import>
        <import>macros_cheetah.xml</import>
    </macros>

                <param name="probthr" type="float" min="0" value="0.001" label="Outlier Probability Threshold" help="Probability threshold for the above specified minimum number of genes to be an outlier cell. This probability is computed from a negative binomial background model of expression in a cluster" />
                <param name="outdistquant" type="float" min="0" max="1" value="0.95" label="Outlier Distance Quantile" help="Outlier cells are merged to outlier clusters if their distance smaller than the outdistquant-quantile of the distance distribution of pairs of cells in the orginal clusters after outlier removal" />
                <!-- RFCorrect -->
                <param name="nbtree" type="integer" optional="true" label="Number of trees to be built" /><!-- 0:Null -->
                <param name="nbfactor" type="integer" min="0" value="5" label="Tree Factor" help="Number of trees based on the number of cells multiplied by this factor. Effective only if the number of trees parameter is set to 0" />
                <!-- <param name="rfseed" type="integer" value="12345" label="Random Seed" /> -->
            </expand>
        </section>
        <section name="tsne" title="tSNE, FR and UMAP" expanded="true" >
            <!-- CompTSNE -->
            <param name="perplexity" type="integer" min="0" value="30" label="Perplexity" help="Perplexity of the t-SNE map" />