annotate scanpy-scale-data.xml @ 26:4cc9362782b4 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

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_scale_data" name="Scanpy ScaleData" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
  <description>to make expression variance the same for all genes</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-scale-data
    #if $scale_max
        --max-value '${scale_max}'
    #end if
    ${zero_center}
    @SAVE_MATRIX_OPTS@
    @INPUT_OPTS@
    @OUTPUT_OPTS@
]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <expand macro="output_object_params"/>
    <param name="zero_center" type="boolean" checked="true" truevalue="" falsevalue="--no-zero-center"
           label="Zero center data before scaling"/>
    <param name="scale_max" argument="--max-value" type="float" min="0" optional="true" label="Truncate to this value after scaling"/>
    <expand macro="save_matrix_params"/>
  </inputs>

  <outputs>
    <expand macro="output_data_obj" description="Scaled data"/>
  </outputs>

  <tests>
    <test>
      <param name="input_obj_file" value="find_variable_genes.h5"/>
      <param name="input_format" value="anndata"/>
      <param name="output_format" value="anndata"/>
      <param name="zero_center" value="true"/>
      <param name="scale_max" value="10"/>
      <output name="output_h5" ftype="h5">
        <assert_contents>
          <has_h5_keys keys="var/mean"/>
        </assert_contents>
      </output>
    </test>
  </tests>

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

    **What it does**

    Scale data to unit variance and (optionally) zero mean (`scanpy.pp.scale`)

    @HELP@

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