comparison scanpy-neighbours.xml @ 15:3cf0177ed87e draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit fda35ff3ea8609c4bb5e1fd9e58ba70cd5b5a997-dirty"

14:a57b128ea4f6

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
  <description>to derive kNN graph</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

    <conditional name="settings">
      <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
      <when value="true"/>
      <when value="false">
        <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='neighbours' />
        <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>

15:3cf0177ed87e

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
  <description>to derive kNN graph</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

    <conditional name="settings">
      <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
      <when value="true"/>
      <when value="false">
        <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>