annotate scanpy-parameter-iterator.xml @ 9:40feaaed47cf draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit edcca4677d954001b33ad15e22603ea452031d76

<tool id="scanpy_parameter_iterator" name="Scanpy ParameterIterator" version="0.0.1+galaxy1">
    <description>produce an iteration over a defined parameter</description>
    <macros>
      <import>scanpy_macros.xml</import>
    </macros>
    <requirements>
      <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
	 mkdir outputs;
    #if str( $input_type.parameter_values ) == "list_comma_separated_values":
        for param in \$(echo '$input_type.input_values' | sed 's/,/ /g'); do
          echo \$param > outputs/'$parameter_name'_\$param\.txt;
         done
    #else if str( $input_type.parameter_values ) == "step_increase_values":
	     for param in \$(seq '$input_type.start_value' '$input_type.step' '$input_type.end_value'); do
	       echo \$param > outputs/'$parameter_name'_\$param\.txt;
	     done
    #end if   
	    ]]></command>

    <inputs>
      <param type="select" name="parameter_name" label="Choose the format of the expression data" help="Use compressed txt, Scanpy or Seurat objects">
        <option value="perplexity" selected="True">Perplexity</option>
        <option value="resolution">Resolution</option>
      </param> 
      <conditional name="input_type">    
        <param type="select" name="parameter_values" label="Choose the format of the input values" help="step increase values or list of all the parameter values">
          <option value="list_comma_separated_values" selected="True">List of all parameter values to be iterated</option>
          <option value="step_increase_values">Step increase values to be iterated</option>
        </param>
        <when value="list_comma_separated_values">
          <param type="text" value="0.1, 0.3, 0.5, 0.7, 1.0, 2.0, 3.0, 4.0, 5.0" name="input_values" label="User input values" help="List of all comma separated values for the parameter"/>
        </when>
        <when value="step_increase_values">
          <param type="float" value="1" name="start_value" label="Starting value" help="Initial value for the parameter"/>
          <param type="float" value="2" name="step" label="Step" help="Increment to use from first to last value"/>
          <param type="float" value="10" name="end_value" label="Ending value" help="Final value for the parameter. The final value is not included if increments of step don't match the last value."/>
        </when>
      </conditional> 
    </inputs>

    <outputs>
      <collection name="parameter_iteration" type="list" label="Parameter iterated">
        <discover_datasets pattern="__name_and_ext__" directory="outputs"/>
      </collection>
    </outputs>

    <tests>
      <test>
        <param name="parameter_name" value="perplexity"/>
         <conditional name="input_type">
          <param name="parameter_values" value="list_comma_separated_values"/>
          <param name="input_values" value="1, 5, 10"/>
        </conditional>
        <output_collection name="parameter_iteration" count="3">
          <element name="perplexity_1" file="perplexity_1.txt" ftype="txt" compare="sim_size"/>
          <element name="perplexity_5" file="perplexity_5.txt" ftype="txt" compare="sim_size"/>
          <element name="perplexity_10" file="perplexity_10.txt" ftype="txt" compare="sim_size"/>
        </output_collection>
      </test>
    </tests>

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

**What it does**

Given start, step and end, it will iterate parameters for either perplexity or
resolution.

**Inputs**

* Parameter name: either Resolution or Perplexity.
* Starting value: float for Resolution, integer for Perplexity.
* Step: float for Resolution, integer for Perplexity.
* End value: float for Resolution, integer for Perplexity.

**Outputs**

* Collection of parameters to be passed to either Scanpy run tSNE (perplexity) or Scanpy find clusters (resolution).

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