view scanpy-normalise-data.xml @ 0:19805a556cd6 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_normalise_data" name="Scanpy NormaliseData" version="@TOOL_VERSION@+galaxy0">
  <description>to make all cells having the same total expression</description>
  <macros>
    <import>scanpy_macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-normalise-data.py
    -i input.h5
    -f '${input_format}'
    -o output.h5
    -F '${output_format}'
    -s '${scale_factor}'
    #if $save_raw
        '${save_raw}'
    #end if
]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <expand macro="output_object_params"/>
    <param name="scale_factor" argument="--scale-factor" type="float" value="1e4" label="Target number to normalise to"/>
    <param name="save_raw" argument="--save-raw" type="boolean" truevalue="--save-raw" falsevalue="" checked="true" label="Save pre-normalised data"/>
  </inputs>

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

  <tests>
    <test>
      <param name="input_obj_file" value="filter_genes.h5"/>
      <param name="input_format" value="anndata"/>
      <param name="output_format" value="anndata"/>
      <param name="scale_factor" value="1e4"/>
      <param name="save_raw" value="false"/>
      <output name="output_h5" file="normalise_data.h5" ftype="h5" compare="sim_size"/>
    </test>
  </tests>

  <help><![CDATA[
=========================================================
Normalize total counts per cell (`pp.normalize_per_cell`)
=========================================================

Normalize each cell by total counts over all genes, so that every cell has
the same total count after normalization.

Similar functions are used, for example, by Seurat, Cell Ranger or SPRING.

@HELP@

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