comparison scanpy-integrate-combat.xml @ 1:aaf4a7a3dd96 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9028e8fa3761fd640dcace5d36bf9b7d558319f7-dirty"

0:2472523c0c50

<?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"/>

    --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"/>

      <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>
  </tests>

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

1:aaf4a7a3dd96

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_integrate_combat" name="Scanpy ComBat" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
  <description>adjust expression for variables that might introduce batch effect</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

    --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"/>

      <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