Mercurial > repos > ebi-gxa > scanpy_compute_graph

comparison scanpy-neighbours.xml @ 21:5ec3b715809c draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 21707e9160aa5028dcf8fb762506790f8e085153-dirty"
author ebi-gxa
date Mon, 10 May 2021 15:28:19 +0000
parents 1dc0ea7a7e62
children a30d21fd5319
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20:c42c2b540ced 21:5ec3b715809c
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 2 <tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
3 <description>to derive kNN graph</description> 3 <description>to derive kNN graph</description>
4 <macros> 4 <macros>
5 <import>scanpy_macros2.xml</import> 5 <import>scanpy_macros2.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
56 <param name="n_neighbors_file" argument="--n-neighbors" type="data" format="txt,tsv" optional="true" 56 <param name="n_neighbors_file" argument="--n-neighbors" type="data" format="txt,tsv" optional="true"
57 label="File with n_neighbours, use with parameter iterator. Overrides the n_neighbors setting"/> 57 label="File with n_neighbours, use with parameter iterator. Overrides the n_neighbors setting"/>
58 <param name="use_rep" type="select" label="Use the indicated representation"> 58 <param name="use_rep" type="select" label="Use the indicated representation">
59 <option value="X_pca" selected="true">X_pca, use PCs</option> 59 <option value="X_pca" selected="true">X_pca, use PCs</option>
60 <option value="X">X, use normalised expression values</option> 60 <option value="X">X, use normalised expression values</option>
61 <option value="X_diffmap"> X_diffmap, use diffusion map</option>
61 </param> 62 </param>
62 <param name="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/> 63 <param name="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/>
63 <param name="knn" argument="--knn" type="boolean" truevalue="" falsevalue="--no-knn" checked="true" 64 <param name="knn" argument="--knn" type="boolean" truevalue="" falsevalue="--no-knn" checked="true"
64 label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbors)"/> 65 label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbors)"/>
65 <param name="method" argument="--method" type="select" label="Method for calculating connectivity"> 66 <param name="method" argument="--method" type="select" label="Method for calculating connectivity">