comparison IDDecoyProbability.xml @ 12:6b42552b3350 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5

11:74ad806c5780

<?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="2.2.0">
  <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:

#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">

  </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>

12:6b42552b3350

<?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 CTDConverter.-->
<!--Proposed Tool Section: [Utilities]-->
<tool id="IDDecoyProbability" name="IDDecoyProbability" version="2.3.0">
  <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 detect_errors="aggressive"><![CDATA[IDDecoyProbability

#if $param_in:
  -in $param_in
#end if
#if $param_fwd_in:

#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">

  </outputs>
  <help>Estimates peptide probabilities using a decoy search strategy.
WARNING: This util is deprecated.


For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_IDDecoyProbability.html</help>
</tool>