Mercurial > repos > iuc > raceid_clustering

comparison raceid_clustering.xml @ 7:c4f39bf4a068 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit b461ba94158cf4cc793919470b78bd3eb91312eb"
author iuc
date Thu, 02 Dec 2021 16:20:43 +0000
parents a4b734cd253b
children f911a64454fb
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6:a4b734cd253b 7:c4f39bf4a068
1 <tool id="raceid_clustering" name="Clustering using RaceID" version="@VERSION_RACEID@+galaxy@VERSION_WRAPPER@" > 1 <tool id="raceid_clustering" name="Clustering using RaceID" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
2 <description>performs clustering, outlier detection, dimensional reduction</description> 2 <description>performs clustering, outlier detection, dimensional reduction</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <import>macros_cheetah.xml</import> 5 <import>macros_cheetah.xml</import>
6 </macros> 6 </macros>
47 <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" /> 47 <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" />
48 <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" /> 48 <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" />
49 <!-- RFCorrect --> 49 <!-- RFCorrect -->
50 <param name="nbtree" type="integer" optional="true" label="Number of trees to be built" /><!-- 0:Null --> 50 <param name="nbtree" type="integer" optional="true" label="Number of trees to be built" /><!-- 0:Null -->
51 <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" /> 51 <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" />
52 <param name="rfseed" type="integer" value="12345" label="Random Seed" /> 52 <!-- <param name="rfseed" type="integer" value="12345" label="Random Seed" /> -->
53 </expand> 53 </expand>
54 </section> 54 </section>
55 <section name="tsne" title="tSNE, FR and UMAP" expanded="true" > 55 <section name="tsne" title="tSNE, FR and UMAP" expanded="true" >
56 <!-- CompTSNE --> 56 <!-- CompTSNE -->
57 <param name="perplexity" type="integer" min="0" value="30" label="Perplexity" help="Perplexity of the t-SNE map" /> 57 <param name="perplexity" type="integer" min="0" value="30" label="Perplexity" help="Perplexity of the t-SNE map" />