comparison scanpy-neighbours.xml @ 30:22bd5861706d draft default tip

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty

29:f776e3ed3c03

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy93" profile="@PROFILE@">
  <description>to derive kNN graph</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

      <param name="n_neighbors_file" value="n_neighbors.txt"/>
      <param name="n_pcs" value="50"/>
      <param name="knn" value="true"/>
      <param name="random_seed" value="0"/>
      <param name="method" value="umap"/>
      <output name="output_h5" file="compute_graph.h5" ftype="h5" compare="sim_size"/>
    </test>
    <test>
      <param name="input_obj_file" value="run_pca.h5"/>
      <param name="input_format" value="anndata"/>
      <param name="output_format" value="anndata"/>

      <param name="n_neighbors" value="15"/>
      <param name="n_pcs" value="50"/>
      <param name="knn" value="true"/>
      <param name="random_seed" value="0"/>
      <param name="method" value="umap"/>
      <output name="output_h5" file="compute_graph.h5" ftype="h5" compare="sim_size"/>
    </test>
  </tests>

  <help><![CDATA[
=============================================================

30:22bd5861706d

<?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" value="n_neighbors.txt"/>
      <param name="n_pcs" value="50"/>
      <param name="knn" value="true"/>
      <param name="random_seed" value="0"/>
      <param name="method" value="umap"/>
      <output name="output_h5" file="compute_graph.h5" ftype="h5" compare="sim_size" delta_frac="0.1"/>
    </test>
    <test>
      <param name="input_obj_file" value="run_pca.h5"/>
      <param name="input_format" value="anndata"/>
      <param name="output_format" value="anndata"/>

      <param name="n_neighbors" value="15"/>
      <param name="n_pcs" value="50"/>
      <param name="knn" value="true"/>
      <param name="random_seed" value="0"/>
      <param name="method" value="umap"/>
      <output name="output_h5" file="compute_graph.h5" ftype="h5" compare="sim_size" delta_frac="0.1"/>
    </test>
  </tests>

  <help><![CDATA[
=============================================================