comparison scanpy-parameter-iterator.xml @ 12:7c4d44c14ceb draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit dcb8b19d34c3e2bf822996ca2e80de111c30b27e"

11:645f12f44a6d

<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>

	     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>

    <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.

12:7c4d44c14ceb

<tool id="scanpy_parameter_iterator" name="Scanpy ParameterIterator" version="0.0.1+galaxy2">
    <description>produce an iteration over a defined parameter</description>
    <macros>
      <import>scanpy_macros.xml</import>
    </macros>
    <requirements>

	     done
    #end if   
	    ]]></command>

    <inputs>
      <param type="select" name="parameter_name" label="Parameter name" help="Select a type of parameter">
        <option value="perplexity" selected="True">Perplexity</option>
        <option value="resolution">Resolution</option>
        <option value="n_neighbors">Number of neighbors</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>

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

**What it does**

Given start, step and end, it will iterate parameters for either perplexity (for t-SNE), resolution (clustering)
or number of neighbours (neighbour graph construction).

**Inputs**

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