annotate scanpy-run-diffmap.xml @ 7:3f8d10b43598 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit cbe12e02ee9ff5692be7547bdbe28fd1cd013a92

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_run_diffmap" name="Scanpy DiffusionMap" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
  <description>calculate diffusion components</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-cli embed diffmap
    --n-comps ${n_comps}
#if $use_graph
    --use-graph '${use_graph}'
#end if
#if $key_added
    --key-added '${key_added}'
#end if
    $export_embed
    @INPUT_OPTS@
    @OUTPUT_OPTS@
]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <expand macro="output_object_params"/>

    <param name="n_comps" argument="--n-comps" type="integer" min="2" value="10"
           label="Number of diffusion components to calculate"/>
    <param name="export_embed" argument="--export-embedding" type="boolean" checked="false"
           truevalue="--export-embedding embed.tsv" falsevalue=""
           label="Export embeddings as a tab-separated text table"/>
    <param name="use_graph" argument="--use-graph" value="neighbors" type="text"
           label="Name of the slot that holds the KNN graph"/>
    <param name="key_added" argument="--key-added" type="text" optional="true"
           label="Additional suffix to the name of the slot to save the calculated trajectory"/>
  </inputs>

  <outputs>
    <expand macro="output_data_obj" description="Diffussion Map"/>
    <data name="output_embed" format="tsv" from_work_dir="embed.tsv" label="${tool.name} on ${on_string}: diffmap embedding">
      <filter>export_embed</filter>
    </data>
  </outputs>

  <tests>
    <test>
      <param name="input_obj_file" value="diffmap.h5"/>
      <param name="input_format" value="anndata"/>
      <param name="output_format" value="anndata"/>
      <param name="n_dcs" value="10"/>
      <param name="root_attr" value="leiden"/>
      <param name="root_value" value="1"/>
      <param name="use_graph" value="neighbors"/>
      <output name="output_h5" file="paga.h5" ftype="h5" compare="sim_size"/>
    </test>
  </tests>

  <help><![CDATA[
====================================================
Calculate Diffusion Components (`scanpy.tl.diffmap`)
====================================================

Calculate diffusion components from single cell KNN graphs.

This requires to run `Scanpy ComputeGraph`, first.

It yields `X_diffmap`, the dimension-reduced representation in diffusion
components space.

@HELP@

@VERSION_HISTORY@
]]></help>
  <expand macro="citations">
    <citation type="doi">10.1186/s13059-019-1663-x</citation>
  </expand>
</tool>