annotate DecoyDatabase.xml @ 9:2e19b070f997 draft

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

<?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="DecoyDatabase" name="DecoyDatabase" version="2.3.0">
  <description>Create decoy protein DB from forward protein DB.</description>
  <macros>
    <token name="@EXECUTABLE@">DecoyDatabase</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[DecoyDatabase

-in
  #for token in $param_in:
    $token
  #end for
#if $param_out:
  -out $param_out
#end if
#if $param_decoy_string:
  -decoy_string     "$param_decoy_string"
#end if
#if $param_decoy_string_position:
  -decoy_string_position
  #if " " in str($param_decoy_string_position):
    "$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"
  #else
    $param_method
  #end if
#end if
#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="fasta" multiple="true" optional="False" size="30" label="Input FASTA file(s), each containing a database" help="(-in) It is recommended to include a contaminant database as well">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_decoy_string" type="text" size="30" value="DECOY_" label="String that is combined with the accession of the protein identifier to indicate a decoy protein" help="(-decoy_string) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </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">
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="fasta"/>
  </outputs>
  <tests>
    <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 https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_DecoyDatabase.html</help>
</tool>