--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy-parameter-iterator.xml	Wed Apr 03 11:07:24 2019 -0400
@@ -0,0 +1,86 @@
+<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>