diff FFEval.xml @ 0:44d9229ac23d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FFEval.xml	Wed Mar 01 12:26:26 2017 -0500
@@ -0,0 +1,64 @@
+<?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="2.1.0">
+  <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
+
+#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
+#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) "/>
+    <expand macro="advanced_options">
+      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="featurexml"/>
+    <data name="param_out_roc" format="tabular"/>
+  </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</help>
+</tool>