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

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

--- a/FFEval.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/FFEval.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,43 +1,65 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="FFEval" name="FFEval" version="1.12.0">
-  <description>Evaluation tool for feature detection algorithms.</description>
-  <macros>
-    <token name="@EXECUTABLE@">FFEval</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>FFEval
+<?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="FFEval" name="FFEval" version="2.0.0">
+    <description>Evaluation tool for feature detection algorithms.</description>
+    <macros>
+      <token name="@EXECUTABLE@">FFEval</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>FFEval
 
--in ${param_in}
--truth ${param_truth}
--rt_tol ${param_rt_tol}
--rt_tol_abs ${param_rt_tol_abs}
--mz_tol ${param_mz_tol}
--out ${param_out}
--abort_reasons ${param_abort_reasons}
--out_roc ${param_out_roc}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_truth:
+  -truth $param_truth
+#end if
+#if $param_rt_tol:
+  -rt_tol $param_rt_tol
+#end if
+#if $param_rt_tol_abs:
+  -rt_tol_abs $param_rt_tol_abs
+#end if
+#if $param_mz_tol:
+  -mz_tol $param_mz_tol
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_abort_reasons:
+  -abort_reasons $param_abort_reasons
+#end if
+#if $param_out_roc:
+  -out_roc $param_out_roc
+#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="featureXML" optional="False" label="Feature input file, which contains the data to be tested against the truth file." help="(-in)"/>
-    <param name="param_truth" type="data" format="featureXML" optional="False" label="Truth feature file that defines what features should be found." help="(-truth)"/>
-    <param name="param_rt_tol" type="float" min="0.0" optional="True" value="0.3" label="Allowed tolerance of RT relative to average feature RT span." help="(-rt_tol)"/>
-    <param name="param_rt_tol_abs" type="float" min="-1.0" optional="True" value="-1.0" label="Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero)." help="(-rt_tol_abs)"/>
-    <param name="param_mz_tol" type="float" min="0.0" optional="True" value="0.25" label="Allowed tolerance in m/z (is divided by charge)." help="(-mz_tol)"/>
-    <param name="param_abort_reasons" type="data" format="featureXML" optional="True" label="Feature file containing seeds with abort reasons." help="(-abort_reasons)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="Feature output file. If given, an annotated input file is written." format="featureXML"/>
-    <data name="param_out_roc" label="If given, a ROC curve file is created (ROC points based on intensity threshold)" format="tabular"/>
-  </outputs>
-  <help>**What it does**
-
-Evaluation tool for feature detection algorithms.
+    <inputs>
+      <param format="xml" help="(-in) " label="Feature input file, which contains the data to be tested against the truth file" name="param_in" optional="False" type="data"/>
+      <param format="xml" help="(-truth) " label="Truth feature file that defines what features should be found" name="param_truth" optional="False" type="data"/>
+      <param help="(-rt_tol) " label="Allowed tolerance of RT relative to average feature RT span" min="0.0" name="param_rt_tol" optional="True" type="float" value="0.3"/>
+      <param help="(-rt_tol_abs) " label="Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero)" min="-1.0" name="param_rt_tol_abs" optional="True" type="float" value="-1.0"/>
+      <param help="(-mz_tol) " label="Allowed tolerance in m/z (is divided by charge)" min="0.0" name="param_mz_tol" optional="True" type="float" value="0.25"/>
+      <param format="xml" help="(-abort_reasons) " label="Feature file containing seeds with abort reasons" name="param_abort_reasons" optional="True" type="data"/>
+      <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="xml" name="param_out"/>
+      <data format="tabular" name="param_out_roc"/>
+    </outputs>
+    <help>Evaluation tool for feature detection algorithms.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_FFEval.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_FFEval.html</help>
+  </tool>