Mercurial > repos > iuc > schicexplorer_schiccluster
changeset 3:3728380d1dff draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit c535679b4086f5bd1a75e9765b8708bf1bd2d81b
| author | iuc |
|---|---|
| date | Thu, 31 Jul 2025 16:51:03 +0000 |
| parents | baa3ae7ac42c |
| children | |
| files | macros.xml scHicCluster.xml |
| diffstat | 2 files changed, 14 insertions(+), 7 deletions(-) [+] |
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--- a/macros.xml Fri Apr 14 14:29:00 2023 +0000 +++ b/macros.xml Thu Jul 31 16:51:03 2025 +0000 @@ -3,6 +3,12 @@ <token name="@TOOL_VERSION@">4</token> <token name="@PROFILE@">22.05</token> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">hicexplorer</xref> + </xrefs> + </xml> + <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">schicexplorer</requirement> @@ -173,4 +179,4 @@ <option value="plasma_r">plasma reversed</option> </param> </xml> -</macros> \ No newline at end of file +</macros>
--- a/scHicCluster.xml Fri Apr 14 14:29:00 2023 +0000 +++ b/scHicCluster.xml Thu Jul 31 16:51:03 2025 +0000 @@ -4,6 +4,7 @@ <token name="@BINARY@">scHicCluster</token> <import>macros.xml</import> </macros> + <expand macro="xrefs"/> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @BINARY@ @@ -29,7 +30,7 @@ ]]></command> <inputs> - + <expand macro="matrix_scooler_macro"/> <param name="clusterMethod_selector" type="select" label="Cluster method:"> <option value="kmeans" selected="True">K-means</option> @@ -40,8 +41,8 @@ <option value="knn" >Exact k-nearest neighbors</option> <option value="pca" >Principal components</option> </param> - <param name="numberOfClusters" type="integer" value="7" label="Number of clusters" help='How many clusters should be computed by kmeans or spectral clustering' /> - <param name="numberOfNearestNeighbors" type="integer" value="100" label="Number of nearest neighbors" help='How many nearest neighbors should be computed for the k-nn graph?' /> + <param name="numberOfClusters" type="integer" value="7" label="Number of clusters" help='How many clusters should be computed by kmeans or spectral clustering' /> + <param name="numberOfNearestNeighbors" type="integer" value="100" label="Number of nearest neighbors" help='How many nearest neighbors should be computed for the k-nn graph?' /> <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/> </inputs> @@ -85,9 +86,9 @@ Clustering on raw data ====================== -scHicCluster uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle. -The clustering can be run on the raw data, on a kNN computed via the exact euclidean distance or via PCA. -Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite such as `scHicCluster`, `scHicClusterMinHash` and `scHicClusterSVL`. +scHicCluster uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle. +The clustering can be run on the raw data, on a kNN computed via the exact euclidean distance or via PCA. +Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite such as `scHicCluster`, `scHicClusterMinHash` and `scHicClusterSVL`. They can give you better results, can be faster or less memory demanding. For more information about scHiCExplorer please consider our documentation on readthedocs.io_