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

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 21707e9160aa5028dcf8fb762506790f8e085153-dirty"

20:c42c2b540ced

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
  <description>to derive kNN graph</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

        <param name="n_neighbors_file" argument="--n-neighbors" type="data" format="txt,tsv" optional="true"
               label="File with n_neighbours, use with parameter iterator. Overrides the n_neighbors setting"/>
        <param name="use_rep" type="select" label="Use the indicated representation">
          <option value="X_pca" selected="true">X_pca, use PCs</option>
          <option value="X">X, use normalised expression values</option>
        </param>
        <param name="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/>
        <param name="knn" argument="--knn" type="boolean" truevalue="" falsevalue="--no-knn" checked="true"
               label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbors)"/>
        <param name="method" argument="--method" type="select" label="Method for calculating connectivity">

21:5ec3b715809c

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
  <description>to derive kNN graph</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

        <param name="n_neighbors_file" argument="--n-neighbors" type="data" format="txt,tsv" optional="true"
               label="File with n_neighbours, use with parameter iterator. Overrides the n_neighbors setting"/>
        <param name="use_rep" type="select" label="Use the indicated representation">
          <option value="X_pca" selected="true">X_pca, use PCs</option>
          <option value="X">X, use normalised expression values</option>
          <option value="X_diffmap"> X_diffmap, use diffusion map</option>
        </param>
        <param name="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/>
        <param name="knn" argument="--knn" type="boolean" truevalue="" falsevalue="--no-knn" checked="true"
               label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbors)"/>
        <param name="method" argument="--method" type="select" label="Method for calculating connectivity">