annotate scanpy-filter-cells.xml @ 0:9f0ca1641ab2 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 9bf9a6e46a330890be932f60d1d996dd166426c4

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_filter_cells" name="Scanpy FilterCells" version="@TOOL_VERSION@+galaxy0">
  <description>based on counts and numbers of genes expressed</description>
  <macros>
    <import>scanpy_macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-filter-cells.py
    -i input.h5
    -f '${input_format}'
    -o output.h5
    -F '${output_format}'
    #if $parameters
        #set pars = ','.join([str($p['name']) for $p in $parameters])
        -p '${pars}'
        #set mins = ','.join([str($p['min']) for $p in $parameters])
        -l '${mins}'
        #set maxs = ','.join([str($p['max']) for $p in $parameters])
        -j '${maxs}'
    #end if
    #if $subset
        -s '${subset}'
    #end if
    ]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <expand macro="output_object_params"/>
    <repeat name="parameters" title="Parameters used to filter cells" min="1">
      <param name="name" type="text" value="n_genes" label="Name of parameter to filter on" help="for example n_genes or n_counts">
        <option value="n_genes">n_genes</option>
        <option value="n_counts">n_counts</option>
      </param>
      <param name="min" type="float" value="0" min="0" label="Min value"/>
      <param name="max" type="float" value="1e9" label="Max value"/>
    </repeat>
    <param name="subset" argument="--subset-list" type="data" format="tsv" optional="true" label="List of barcodes"/>
  </inputs>

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

  <tests>
    <test>
      <param name="input_obj_file" value="read_10x.h5"/>
      <param name="input_format" value="anndata"/>
      <param name="output_format" value="anndata"/>
      <repeat name="parameters">
        <param name="name" value="n_genes"/>
        <param name="min" value="200"/>
        <param name="max" value="2500"/>
      </repeat>
      <repeat name="parameters">
        <param name="name" value="n_counts"/>
        <param name="min" value="0"/>
        <param name="max" value="1e9"/>
      </repeat>
      <output name="output_h5" file="filter_cells.h5" ftype="h5" compare="sim_size"/>
    </test>
  </tests>

  <help><![CDATA[
========================================================================================
Filter cells outliers based on counts and numbers of genes expressed (`pp.filter_cells`)
========================================================================================

For instance, only keep cells with at least `min_counts` counts or
`min_genes` genes expressed. This is to filter measurement outliers, i.e.,
"unreliable" observations.

@HELP@

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