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

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

--- a/PTPredict.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/PTPredict.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,35 +1,49 @@
-<?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
+<?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: [Peptide property prediction]-->
+  <tool id="PTPredict" name="PTPredict" version="2.0.0">
+    <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="references"/>
+    <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} 
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_svm_model:
+  -svm_model $param_svm_model
+#end if
+#if $param_max_number_of_peptides:
+  -max_number_of_peptides $param_max_number_of_peptides
+#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_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
+    <inputs>
+      <param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
+      <param format="txt" help="(-svm_model) " label="svm model in libsvm format (can be produced by PTModel)" name="param_svm_model" optional="False" type="data"/>
+      <param help="(-max_number_of_peptides) &lt;br&gt;" label="the maximum number of peptides considered at once (bigger number will lead to faster results but needs more memory)" name="param_max_number_of_peptides" type="integer" value="100000"/>
+      <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"/>
+    </outputs>
+    <help>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>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PTPredict.html</help>
+  </tool>