diff ConsensusMapNormalizer.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

--- a/ConsensusMapNormalizer.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/ConsensusMapNormalizer.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,39 +1,58 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="ConsensusMapNormalizer" name="ConsensusMapNormalizer" version="1.12.0">
-  <description>Normalizes maps of one consensusXML file</description>
-  <macros>
-    <token name="@EXECUTABLE@">ConsensusMapNormalizer</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>ConsensusMapNormalizer
+<?xml version="1.0" encoding="UTF-8"?>
+  <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+  <!--Proposed Tool Section: [Map Alignment]-->
+  <tool id="ConsensusMapNormalizer" name="ConsensusMapNormalizer" version="2.0.0">
+    <description>Normalizes maps of one consensusXML file</description>
+    <macros>
+      <token name="@EXECUTABLE@">ConsensusMapNormalizer</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>ConsensusMapNormalizer
 
--in ${param_in}
--out ${param_out}
--algorithm_type ${param_algorithm_type}
--ratio_threshold ${param_ratio_threshold}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_algorithm_type:
+  -algorithm_type
+  #if &quot; &quot; in str($param_algorithm_type):
+    &quot;$param_algorithm_type&quot;
+  #else
+    $param_algorithm_type
+  #end if
+#end if
+#if $param_ratio_threshold:
+  -ratio_threshold $param_ratio_threshold
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="consensusXML" optional="False" label="input file" help="(-in)"/>
-    <param name="param_algorithm_type" type="select" optional="True" value="robust_regression" label="The normalization algorithm that is applied." help="(-algorithm_type)">
-      <option value="robust_regression">robust_regression</option>
-      <option value="median">median</option>
-      <option value="quantile">quantile</option>
-    </param>
-    <param name="param_ratio_threshold" type="float" min="0.001" max="1.0" optional="True" value="0.67" label="Only for 'robust_regression': the parameter is used to distinguish between non-outliers (ratio_threshold &lt; intensity ratio &lt; 1/ratio_threshold) and outliers." help="(-ratio_threshold)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output file" format="consensusXML"/>
-  </outputs>
-  <help>**What it does**
-
-Normalizes maps of one consensusXML file
+    <inputs>
+      <param format="consensusxml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
+      <param help="(-algorithm_type) " label="The normalization algorithm that is applied" name="param_algorithm_type" optional="True" type="select" value="robust_regression">
+        <option value="robust_regression">robust_regression</option>
+        <option value="median">median</option>
+        <option value="quantile">quantile</option>
+      </param>
+      <param help="(-ratio_threshold) " label="Only for 'robust_regression': the parameter is used to distinguish between non-outliers (ratio_threshold &lt; intensity ratio &lt; 1/ratio_threshold) and outliers" max="1.0" min="0.001" name="param_ratio_threshold" optional="True" type="float" value="0.67"/>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="consensusxml" name="param_out"/>
+    </outputs>
+    <help>Normalizes maps of one consensusXML file
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusMapNormalizer.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ConsensusMapNormalizer.html</help>
+  </tool>