comparison scanpy-regress-variable.xml @ 1:203fac3b1ba3 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1cc5d2101b8b14fa99e11b01714e5544704e669f

0:6c990f8ccad3

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_regress_variable" name="Scanpy RegressOut" version="@TOOL_VERSION@+galaxy0">
  <description>variables that might introduce batch effect</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-regress
    --keys '${variable_keys}'
    @INPUT_OPTS@
    @OUTPUT_OPTS@
]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <expand macro="output_object_params"/>
    <param name="variable_keys" type="text" label="Variables to regress out" help="Use comma to separate multiple variables"/>
  </inputs>

  <outputs>
    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Scaled data"/>
  </outputs>

1:203fac3b1ba3

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_regress_variable" name="Scanpy RegressOut" version="@TOOL_VERSION@+galaxy1">
  <description>variables that might introduce batch effect</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
#if $variable_keys
  ln -s '${input_obj_file}' input.h5 &&
  PYTHONIOENCODING=utf-8 scanpy-regress
      --keys '${variable_keys}'
      @INPUT_OPTS@
      @OUTPUT_OPTS@
#else
  echo "No regression variables passed, simply passing original input as output unchanged.";
  cp '${input_obj_file}' '${output_h5}'
#end if
]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <expand macro="output_object_params"/>
    <param name="variable_keys" type="text" label="Variables to regress out" help="Use comma to separate multiple variables. Not supplying variables will simply pass the input data as output unchanged.">
      <sanitizer>
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
  </inputs>

  <outputs>
    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Scaled data"/>
  </outputs>