<?xml version="1.0" encoding="utf-8"?>
<tool id="monocle3_partition" name="Monocle3 partition" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
  <description>of cells into groups</description>
  <macros>
    <import>monocle3-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
LANG=en_US.UTF-8 monocle3 partition
    --reduction-method '${reduction_method}'
#if $knn
    --knn '${knn}'
#end if
#if $weight
    --weight
#end if
#if $louvain_iter
    --louvain-iter '${louvain_iter}'
#end if
#if $resolution
    --resolution '${resolution}'
#end if
#if $partition_qval
    --partition-qval '${partition_qval}'
#end if

    @INPUT_OPTS@
    @OUTPUT_OPTS@

    @VERBOSE@
]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <expand macro="output_object_params"/>
    <param name="reduction_method" argument="--reduction-method" type="select" label="The dimensionality reduction to base the clustering on.">
      <option selected="true" value="UMAP">UMAP</option>
      <option value="tSNE">tSNE</option>
      <option value="PCA">PCA</option>
      <option value="LSI">LSI</option>
    </param>
    <param name="knn" argument="--knn" optional="true" type="integer" value="20" label="Number of nearest neighbours used for Louvain clustering."/>
    <param name="weight" argument="--weight" type="boolean" checked="false" label="When this option is set, calculate the weight for each edge in the kNN graph."/>
    <param name="louvain_iter" argument="--louvain-iter" optional="true" type="integer" value="1" label="The number of iterations for Louvain clustering."/>
    <param name="resolution" argument="--resolution" optional="true" type="float" label="Resolution of clustering result, specifying the granularity of clusters. Not used by default and the standard igraph louvain clustering algorithm will be used."/>
    <param name="partition_qval" argument="--partition-qval" optional="true" type="float" value="0.05" label="The q-value threshold used to determine the partition of cells."/>
    <expand macro="verbose_flag"/>
  </inputs>

  <outputs>
    <data name="output_rds" format="rdata" from_work_dir="output.RDS" label="${tool.name} on ${on_string}: ${output_object_format}"/>
  </outputs>

  <tests>
    <test>
      <param name="input_object_file" value="input.RDS"/>
      <param name="input_object_format" value="cds3"/>
      <param name="reduction_method" value="UMAP"/>
      <param name="knn" value="20"/>
      <param name="louvain_iter" value="1"/>
      <param name="partition_qval" value="0.05"/>
      <param name="output_object_format" value="cds3"/>
      <output name="output_rds" file="output.rds" ftype="rdata" compare="sim_size"/>
    </test>
  </tests>

  <help><![CDATA[
==============================================
Monocle3 clustering of cells (`cluster_cells`)
==============================================

Cluster the primary dimensionality reduced space

@HELP@

@VERSION_HISTORY@
]]></help>
  <expand macro="citations"/>
</tool>