comparison DecoyDatabase.xml @ 3:178e00cf12d7 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

2:8ced1ef014ae

<?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="DecoyDatabase" name="DecoyDatabase" version="2.1.0">
  <description>Create decoy peptide databases from normal ones.</description>
  <macros>
    <token name="@EXECUTABLE@">DecoyDatabase</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>

    "$param_decoy_string_position"
  #else
    $param_decoy_string_position
  #end if
#end if
#if $param_append:
  -append
  #if " " in str($param_append):
    "$param_append"
  #else
    $param_append
  #end if
#end if
#if $param_method:
  -method
  #if " " in str($param_method):
    "$param_method"

    </param>
    <param name="param_decoy_string_position" display="radio" type="select" optional="False" value="prefix" label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" help="(-decoy_string_position) ">
      <option value="prefix" selected="true">prefix</option>
      <option value="suffix">suffix</option>
    </param>
    <param name="param_append" display="radio" type="select" optional="False" value="true" label="If this flag is used, the decoy database is appended to the target database, allowing combined target decoy searches" help="(-append) ">
      <option value="true" selected="true">true</option>
      <option value="false">false</option>
    </param>
    <param name="param_method" display="radio" type="select" optional="False" value="reverse" label="Method by which decoy sequences are generated from target sequences" help="(-method) ">
      <option value="reverse" selected="true">reverse</option>
      <option value="shuffle">shuffle</option>
    </param>
    <expand macro="advanced_options">

    <test>
        <param name="param_in" value="DecoyDatabase_input.fasta"/>
        <output name="param_out" file="DecoyDatabase_output.fasta"/>
    </test>
  </tests>
  <help>Create decoy peptide databases from normal ones.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html</help>
</tool>

3:178e00cf12d7

<?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="DecoyDatabase" name="DecoyDatabase" version="2.2.0">
  <description>Create decoy protein DB from forward protein DB.</description>
  <macros>
    <token name="@EXECUTABLE@">DecoyDatabase</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>

    "$param_decoy_string_position"
  #else
    $param_decoy_string_position
  #end if
#end if
#if $param_only_decoy:
  -only_decoy
#end if
#if $param_method:
  -method
  #if " " in str($param_method):
    "$param_method"

    </param>
    <param name="param_decoy_string_position" display="radio" type="select" optional="False" value="prefix" label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" help="(-decoy_string_position) ">
      <option value="prefix" selected="true">prefix</option>
      <option value="suffix">suffix</option>
    </param>
    <param name="param_only_decoy" display="radio" type="boolean" truevalue="-only_decoy" falsevalue="" checked="false" optional="True" label="Write only decoy proteins to the output database instead of a combined database" help="(-only_decoy) "/>
    <param name="param_method" display="radio" type="select" optional="False" value="reverse" label="Method by which decoy sequences are generated from target sequences" help="(-method) ">
      <option value="reverse" selected="true">reverse</option>
      <option value="shuffle">shuffle</option>
    </param>
    <expand macro="advanced_options">

    <test>
        <param name="param_in" value="DecoyDatabase_input.fasta"/>
        <output name="param_out" file="DecoyDatabase_output.fasta"/>
    </test>
  </tests>
  <help>Create decoy protein DB from forward protein DB.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html</help>
</tool>