comparison scanpy-neighbours.xml @ 23:bc9e8de21efb draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4332e90fa9f269bf4a8b912366eeace9c040b4c4-dirty"

22:a30d21fd5319

<?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"/>

    #end if

    --method '${settings.method}'
    --metric '${settings.metric}'
    --random-state '${settings.random_seed}'
    #if $settings.use_rep != "auto"
        --use-rep '${settings.use_rep}'
    #end if
    #if $settings.n_pcs
        --n-pcs '${settings.n_pcs}'
    #end if

        <param name="key_added" argument="--key-added" type="text" optional="true" label="Key added"
            help="If not specified, the neighbors data is stored in .uns[‘neighbors’], distances and connectivities are stored in .obsp[‘distances’] and .obsp[‘connectivities’] respectively. If specified, the neighbors data is added to .uns[key_added], distances are stored in .obsp[key_added+’_distances’] and connectivities in .obsp[key_added+’_connectivities’]." value='' />
        <param name="n_neighbors" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbors used"/>
        <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">
          <option value="umap" selected="true">UMAP</option>

23:bc9e8de21efb

<?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"/>

    #end if

    --method '${settings.method}'
    --metric '${settings.metric}'
    --random-state '${settings.random_seed}'
    #if $settings.use_rep
        --use-rep '${settings.use_rep}'
    #end if
    #if $settings.n_pcs
        --n-pcs '${settings.n_pcs}'
    #end if

        <param name="key_added" argument="--key-added" type="text" optional="true" label="Key added"
            help="If not specified, the neighbors data is stored in .uns[‘neighbors’], distances and connectivities are stored in .obsp[‘distances’] and .obsp[‘connectivities’] respectively. If specified, the neighbors data is added to .uns[key_added], distances are stored in .obsp[key_added+’_distances’] and connectivities in .obsp[key_added+’_connectivities’]." value='' />
        <param name="n_neighbors" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbors used"/>
        <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" argument="--use-rep" type="text" optional="true" label="Use the indicated representation" help="'X' (for the content of .X, usually normalised expression values) or any key for .obsm (e.g. X_pca for PCA) is valid. If not set, the representation is chosen automatically: For .n_vars less than 50, .X is used, otherwise ‘X_pca’ is used. If ‘X_pca’ is not present, it’s computed with default parameters."/>
        <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">
          <option value="umap" selected="true">UMAP</option>