comparison scanpy-integrate-combat.xml @ 15:3c47bc560688 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

14:c6611adc8f4a

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_integrate_combat" name="Scanpy ComBat" version="@TOOL_VERSION@+galaxy93" 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

    <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

15:3c47bc560688

<?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-cli integrate combat 
  --batch-key '${batch_key}'
  #if $batch_layer
    --batch-layer '${batch_layer}'
  #end if
  #if $covariates

    <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" ftype="h5">
        <assert_contents>
          <has_h5_keys keys="layers/combat"/>
        </assert_contents>
      </output>
    </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" delta_frac="0.1"/>
    </test>
  </tests>

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