diff IDDecoyProbability.xml @ 0:99effccd5e83 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/IDDecoyProbability.xml	Wed Mar 01 10:15:23 2017 -0500
@@ -0,0 +1,58 @@
+<?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="IDDecoyProbability" name="IDDecoyProbability" version="2.1.0">
+  <description>Estimates peptide probabilities using a decoy search strategy.
+WARNING: This util is deprecated.</description>
+  <macros>
+    <token name="@EXECUTABLE@">IDDecoyProbability</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>IDDecoyProbability
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_fwd_in:
+  -fwd_in $param_fwd_in
+#end if
+#if $param_rev_in:
+  -rev_in $param_rev_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_decoy_algorithm_number_of_bins:
+  -decoy_algorithm:number_of_bins $adv_opts.param_decoy_algorithm_number_of_bins
+#end if
+    #if $adv_opts.param_decoy_algorithm_lower_score_better_default_value_if_zero:
+  -decoy_algorithm:lower_score_better_default_value_if_zero $adv_opts.param_decoy_algorithm_lower_score_better_default_value_if_zero
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="idxml" optional="True" label="Identification input of combined forward decoy search (reindex with PeptideIndexer first)" help="(-in) "/>
+    <param name="param_fwd_in" type="data" format="idxml" optional="True" label="Identification input of forward run" help="(-fwd_in) "/>
+    <param name="param_rev_in" type="data" format="idxml" optional="True" label="Identification input of decoy run" help="(-rev_in) "/>
+    <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) "/>
+      <param name="param_decoy_algorithm_number_of_bins" type="integer" value="40" label="Number of bins used for the fitting, if sparse datasets are used, this number should be smalle" help="(-number_of_bins) "/>
+      <param name="param_decoy_algorithm_lower_score_better_default_value_if_zero" type="float" value="50.0" label="This value is used if" help="(-lower_score_better_default_value_if_zero) e.g. a E-value score is 0 and cannot be transformed in a real number (log of E-value)"/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="idxml"/>
+  </outputs>
+  <help>Estimates peptide probabilities using a decoy search strategy.
+WARNING: This util is deprecated.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDDecoyProbability.html</help>
+</tool>