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

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

--- a/RTEvaluation.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/RTEvaluation.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,39 +1,57 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="RTEvaluation" name="RTEvaluation" version="1.12.0">
-  <description>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.</description>
-  <macros>
-    <token name="@EXECUTABLE@">RTEvaluation</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>RTEvaluation
+<?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: [Utilities]-->
+  <tool id="RTEvaluation" name="RTEvaluation" version="2.0.0">
+    <description>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.</description>
+    <macros>
+      <token name="@EXECUTABLE@">RTEvaluation</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>RTEvaluation
 
--in ${param_in}
--out ${param_out}
--sequences_file ${param_sequences_file}
-${param_latex}
--p_value_dim_1 ${param_p_value_dim_1}
--p_value_dim_2 ${param_p_value_dim_2}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_sequences_file:
+  -sequences_file $param_sequences_file
+#end if
+#if $param_latex:
+  -latex
+#end if
+#if $param_p_value_dim_1:
+  -p_value_dim_1 $param_p_value_dim_1
+#end if
+#if $param_p_value_dim_2:
+  -p_value_dim_2 $param_p_value_dim_2
+#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="idXML" optional="False" label="input file" help="(-in)"/>
-    <param name="param_sequences_file" type="data" format="fasta" optional="True" label="Filename of a FASTA file containing protein sequences.#br#All peptides that are not a substring of a sequence in this file are considered as false" help="(-sequences_file)"/>
-    <param name="param_latex" type="boolean" truevalue="-latex true" falsevalue="-latex false" checked="false" optional="True" label="indicates whether the output file format of the table should be latex or csv" help="(-latex)"/>
-    <param name="param_p_value_dim_1" type="float" min="0.0" max="1.0" optional="True" value="0.01" label="Significance level of first dimension RT filter" help="(-p_value_dim_1)"/>
-    <param name="param_p_value_dim_2" type="float" min="0.0" max="1.0" optional="True" value="0.05" label="Significance level of second dimension RT filter" help="(-p_value_dim_2)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output file " format="tabular"/>
-  </outputs>
-  <help>**What it does**
-
-Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.
+    <inputs>
+      <param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
+      <param format="fasta" help="(-sequences_file) &lt;br&gt;All peptides that are not a substring of a sequence in this file are considered as false" label="Filename of a FASTA file containing protein sequences" name="param_sequences_file" optional="True" type="data"/>
+      <param checked="false" falsevalue="" help="(-latex) " label="indicates whether the output file format of the table should be latex or csv" name="param_latex" optional="True" truevalue="-latex" type="boolean"/>
+      <param help="(-p_value_dim_1) " label="Significance level of first dimension RT filte" max="1.0" min="0.0" name="param_p_value_dim_1" optional="True" type="float" value="0.01"/>
+      <param help="(-p_value_dim_2) " label="Significance level of second dimension RT filte" max="1.0" min="0.0" name="param_p_value_dim_2" optional="True" type="float" value="0.05"/>
+      <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="tabular" name="param_out"/>
+    </outputs>
+    <help>Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RTEvaluation.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RTEvaluation.html</help>
+  </tool>