diff PTPredict.xml @ 0:3d84209d3178 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PTPredict.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,35 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="PTPredict" name="PTPredict" version="1.12.0">
+  <description>predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel</description>
+  <macros>
+    <token name="@EXECUTABLE@">PTPredict</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>PTPredict
+
+-in ${param_in}
+-out ${param_out}
+-svm_model ${param_svm_model}
+-max_number_of_peptides ${param_max_number_of_peptides}
+-threads \${GALAXY_SLOTS:-24} 
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="idXML" optional="False" label="input file " help="(-in)"/>
+    <param name="param_svm_model" type="data" format="txt" optional="False" label="svm model in libsvm format (can be produced by PTModel)" help="(-svm_model)"/>
+    <param name="param_max_number_of_peptides" type="integer" value="100000" label="the maximum number of peptides considered at once (bigger number will lead to faster results but needs more memory).#br#" help="(-max_number_of_peptides)"/>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="output file#br#" format="idXML"/>
+  </outputs>
+  <help>**What it does**
+
+predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PTPredict.html
+
+@REFERENCES@
+</help>
+</tool>