<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_run_paga" name="Scanpy PAGA" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
  <description>trajectory inference</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-cli paga
    --groups '${groups}'
#if $neighbors_key
    --neighbors-key '${neighbors_key}'
#end if
#if $key_added
    --key-added '${key_added}'
#end if
#if $use_rna_velocity
    --use-rna-velocity
#end if
    @INPUT_OPTS@
    @OUTPUT_OPTS@
]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <expand macro="output_object_params"/>

    <param name="groups" argument="--groups" type="text" label="Name of the clustering"/>
    <param name="neighbors_key" argument="--neighbors-key" value="neighbors" type="text" label="Name of the slot that holds the KNN graph"/>
    <param name="key_added" argument="--key-added" type="text" optional="true" label="Additional suffix to the name of the slot to save the calculated trajectory"/>
    <param name="use_rna_velocity" type="boolean" checked="false" label="Use RNA velocity to orient edges in the abstracted graph and estimate transitions." help=" Requires that adata.uns contains a directed single-cell graph with key velocity_graph. This feature might be subject to change in the future."/>
  </inputs>

  <outputs>
    <expand macro="output_data_obj" description="PAGA object"/>
  </outputs>

  <tests>
    <test>
      <param name="input_obj_file" value="find_cluster.h5"/>
      <param name="input_format" value="anndata"/>
      <param name="output_format" value="anndata"/>
      <param name="groups" value="louvain"/>
      <param name="neighbors_key" value="neighbors"/>
      <output name="output_h5" file="paga.h5" ftype="h5" compare="sim_size"/>
    </test>
  </tests>

  <help><![CDATA[
===================================================================
Perform PAGA (partition-based graph abstraction) (`scanpy.tl.paga`)
===================================================================

Infer trajectories by mapping out the coarse-grained connectivity structures of
complex manifolds of single cell KNN graphs (Wolf et al, 2019).

This requires to run `Scanpy FindCluster`, first.

It yields `paga`, connectivity graph between clusters.

@HELP@

@VERSION_HISTORY@
]]></help>
  <expand macro="citations">
    <citation type="doi">10.1186/s13059-019-1663-x</citation>
  </expand>
</tool>