diff scanpy-parameter-iterator.xml @ 0:86730078be1e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy-scripts commit dca9be719ceb86abad7589c240b1bb7656826c48-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy-parameter-iterator.xml	Wed Mar 13 11:48:57 2019 -0400
@@ -0,0 +1,71 @@
+<tool id="scanpy_parameter_iterator" name="Scanpy ParameterIterator" version="0.0.1+galaxy0">
+    <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;
+	 for param in \$(seq '$start_value' '$step' '$end_value'); do
+	    echo \$param > outputs/'$parameter_name'_\$param\.txt;
+	 done
+	    ]]></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="resolution" selected="true">Resolution</option>
+        <option value="perplexity">Perplexity</option>
+      </param>
+      <param type="float" value="0" name="start_value" label="Starting value" help="Initial value for the parameter"/>
+      <param type="float" value="1" 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."/>
+    </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"/>
+        <param name="start_value" value="1"/>
+        <param name="step" value="1"/>
+        <param name="end_value" value="2"/>
+        <output_collection name="parameter_iteration">
+          <element name="perplexity_1"/>
+          <element name="perplexity_2">
+            <assert_contents>
+              <has_line line="2" />
+            </assert_contents>
+          </element>
+        </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>