view scanpy-multiplet-scrublet-plot.xml @ 0:57310f30da92 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 3365d5d4f7930e736fa6814df36d68e578d45d46-dirty"

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_plot_scrublet" name="Scanpy Plot Scrublet" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
  <description>visualise multiplet scoring distribution</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
ln -s '${input_obj_file}' input.h5 &&
PYTHONIOENCODING=utf-8 scanpy-cli plot scrublet
--scale-hist-obs '${scale_hist_obs}'
--scale-hist-sim '${scale_hist_sim}'
#if $settings.default == "false"
    --fig-size '${settings.fig_size}'
    --fig-dpi ${settings.fig_dpi}
    --fig-fontsize ${settings.fig_fontsize}
#end if    
@INPUT_OPTS@
./output.png
]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <param name="scale_hist_obs" argument="--scale-hist-obs" type="select" label="y axis scale transformation for observed transcriptome plot">
      <option value="log" selected="true">log</option>
      <option value="linear">linear</option>
      <option value="symlog">symlog</option>
      <option value="logit">logit</option>
    </param>
    <param name="scale_hist_sim" argument="--scale-hist-sim" type="select" label="y axis scale transformation for simulated transcriptome plot">
      <option value="log">log</option>
      <option value="linear" selected='true'>linear</option>
      <option value="symlog">symlog</option>
      <option value="logit">logit</option>
    </param>
    <conditional name="settings">
      <param name="default" type="boolean" checked="true" label="Use plot defaults"/>
      <when value="true"/>
      <when value="false">
        <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/>
        <param name="fig_dpi" argument="--fig-dpi" type="integer" min="1" value="80" label="Figure dpi"/>
        <param name="fig_fontsize" argument="--fig-fontsize" type="integer" min="0" value="10" label="Figure font size"/>
      </when>
    </conditional>  
  </inputs>

  <outputs>
    <data name="output_png" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: Scrublet plot"/>
  </outputs>

  <tests>
    <test>
      <param name="input_obj_file" value="scrublet.h5"/>
      <param name="input_format" value="anndata"/>
      <param name="scale_hist_obs" value="linear"/>
      <param name="scale_hist_sim" value="linear"/>
      <output name="output_png" file="plot_scrublet.png" ftype="png" compare="sim_size"/>
    </test>
  </tests>

  <help><![CDATA[
Plot histogram of doublet scores for observed transcriptomes and simulated doublets.

@HELP@

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