annotate DatabaseFilter.xml @ 1:1fed9fa56502 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d2b76821e22b13ed6e21795ac1b82446d8f594c6

<?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="DatabaseFilter" name="DatabaseFilter" version="2.2.0">
  <description>Filters a protein database (FASTA format) based on identified proteins</description>
  <macros>
    <token name="@EXECUTABLE@">DatabaseFilter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>DatabaseFilter

#if $param_in:
  -in $param_in
#end if
#if $param_id:
  -id $param_id
#end if
#if $param_method:
  -method
  #if " " in str($param_method):
    "$param_method"
  #else
    $param_method
  #end if
#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
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="fasta" optional="False" label="Input FASTA file, containing a database" help="(-in) "/>
    <param name="param_id" type="data" format="idxml,mzid" optional="False" label="Input file containing identified peptides and proteins" help="(-id) "/>
    <param name="param_method" display="radio" type="select" optional="False" value="whitelist" label="Switch between white-/blacklisting" help="(-method) ">
      <option value="whitelist" selected="true">whitelist</option>
      <option value="blacklist">blacklist</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>
  <help>Filters a protein database (FASTA format) based on identified proteins


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