diff RTPredict.xml @ 0:3d84209d3178 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RTPredict.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,51 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="RTPredict" name="RTPredict" version="1.12.0">
+  <description>Predicts retention times for peptides using a model trained by RTModel.</description>
+  <macros>
+    <token name="@EXECUTABLE@">RTPredict</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>RTPredict
+
+-in_id ${param_in_id}
+-in_text ${param_in_text}
+-svm_model ${param_svm_model}
+-total_gradient_time ${param_total_gradient_time}
+-threads \${GALAXY_SLOTS:-24} 
+-out_id:file ${param_file}
+-out_id:positive ${param_positive}
+-out_id:negative ${param_negative}
+-out_text:file ${param_file}
+#if $adv_opts.adv_opts_selector=='advanced':
+    -max_number_of_peptides ${adv_opts.param_max_number_of_peptides}
+    ${adv_opts.param_rewrite_peptideidentification_rtmz}
+#end if
+</command>
+  <inputs>
+    <param name="param_in_id" type="data" format="idXML" optional="True" label="Peptides with precursor information" help="(-in_id)"/>
+    <param name="param_in_text" type="data" format="txt" optional="True" label="Peptides as text-based file" help="(-in_text)"/>
+    <param name="param_svm_model" type="data" format="txt" optional="False" label="svm model in libsvm format (can be produced by RTModel)" help="(-svm_model)"/>
+    <param name="param_total_gradient_time" type="float" min="1e-05" optional="True" value="1.0" label="The time (in seconds) of the gradient (peptide RT prediction)" help="(-total_gradient_time)"/>
+    <expand macro="advanced_options">
+      <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)." help="(-max_number_of_peptides)"/>
+      <param name="param_rewrite_peptideidentification_rtmz" type="boolean" truevalue="-out_id:rewrite_peptideidentification_rtmz true" falsevalue="-out_id:rewrite_peptideidentification_rtmz false" checked="false" optional="True" label="Rewrites each peptideidentification's rt and mz from prediction and calculation (according to the best hit)" help="(-rewrite_peptideidentification_rtmz)"/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_file" label="Output file with peptide RT prediction" format="idXML"/>
+    <data name="param_positive" label="Output file in idXML format containing positive predictions for peptide separation prediction - requires 'out_id:negative' to be present as well." format="idXML"/>
+    <data name="param_negative" label="Output file in idXML format containing negative predictions for peptide separation prediction - requires 'out_id:positive' to be present as well." format="idXML"/>
+    <data name="param_file" label="Output file with predicted RT values" format="tabular"/>
+  </outputs>
+  <help>**What it does**
+
+Predicts retention times for peptides using a model trained by RTModel.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTPredict.html
+
+@REFERENCES@
+</help>
+</tool>