comparison scanpy-neighbours.xml @ 13:e6c989a9211c draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e572b5425460d57f1bd13ab6374674c1c6801ab3-dirty"

12:c78c930e3263

<?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"/>
  <command detect_errors="exit_code"><![CDATA[
ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-neighbors
#if $settings.default == "false"
    #if $settings.n_neighbors_file
        --n-neighbors \$( cat $settings.n_neighbors_file )
    #elif $settings.n_neighbors
        --n-neighbors '${settings.n_neighbors}'
    #end if
    --method '${settings.method}'
    --metric '${settings.metric}'
    --random-state '${settings.random_seed}'
    #if $settings.use_rep != "auto"
        --use-rep '${settings.use_rep}'

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

13:e6c989a9211c

<?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"/>
  <command detect_errors="exit_code"><![CDATA[
#from pathlib import Path
#if $settings.n_neighbors_file
    #set n_neighbors = Path($settings.n_neighbors_file.__str__).read_text().strip()
#elif $settings.n_neighbors
    #set n_neighbors = $settings.n_neighbors.__str__.strip()
#end if

ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-neighbors
#if $settings.default == "false"
    #if $n_neighbors
        --n-neighbors $n_neighbors
    #end if
    #if $settings.key_added
        #set key_added = $settings.key_added
        #if $n_neighbors
            #set key_added = $key_added.replace('N_NEIGHBORS', $n_neighbors.__str__)
        #end if
        --key-added '${key_added}'
    #end if

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

    <expand macro="output_object_params"/>
    <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>