diff RTEvaluation.xml @ 0:3d84209d3178 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RTEvaluation.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,39 @@
+<?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
+
+-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} 
+</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.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RTEvaluation.html
+
+@REFERENCES@
+</help>
+</tool>