<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_integrate_combat" name="Scanpy ComBat" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
  <description>adjust expression for variables that might introduce batch effect</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
#if $batch_key
  ln -s '${input_obj_file}' input.h5 &&
  PYTHONIOENCODING=utf-8 scanpy-integrate combat 
  --batch-key '${batch_key}'
  #if $batch_layer
    --batch-layer '${batch_layer}'
  #end if
  #if $covariates
    --covariates '${$covariates}'
  #end if
  #if $key_added
    --key-added '${key_added}'
  #end if
  @INPUT_OPTS@
  @OUTPUT_OPTS@
#else
  echo "No batch variables passed, simply passing original input as output unchanged." && cp '${input_obj_file}' output.h5
#end if
]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <expand macro="output_object_params"/>
    <param name="batch_key" type="text" argument="--batch-key" label="The name of the column in adata.obs that differentiates among experiments/batches.">
      <sanitizer>
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param name="batch_layer" type="text" argument="--batch-layer" label="Layer to batch correct. By default corrects the contents of .X.">
      <sanitizer>
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param name="covariates" argument="--covariates" type="text" label="Comma separated list of additional covariates besides the batch variable such as adjustment variables or biological condition." help="This parameter refers to the design matrix X in Equation 2.1 in [Johnson07] and to the mod argument in the original combat function in the sva R package. Note that not including covariates may introduce bias or lead to the removal of biological signal in unbalanced designs.">
      <sanitizer>
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param name="key_added" argument="--key-added" type="text" optional="true"
        label="Key under which to add the computed results." help="By default a new layer will be created called 'combat', 'combat_{layer}' or 'combat_{layer}_{key_added}' where those parameters were specified. A value of 'X' causes batch-corrected values to overwrite the original content of .X."/>
  </inputs>

  <outputs>
    <expand macro="output_data_obj" description="Batch-corrected for ${batch_key}"/>
  </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="batch_key" value="louvain"/>
      <output name="output_h5" file="combat.h5" ftype="h5" compare="sim_size"/>
    </test>
    <test>
      <param name="input_obj_file" value="find_cluster.h5"/>
      <param name="input_format" value="anndata"/>
      <param name="output_format" value="anndata"/>
      <output name="output_h5" file="combat_copy.h5" ftype="h5" compare="sim_size"/>
    </test>
  </tests>

  <help><![CDATA[
    .. class:: infomark

    **What it does**

    Corrects for batch effects by fitting linear models, gains statistical power via an EB framework where information is borrowed across genes.

    @HELP@

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