mobyle-programs 5.1.1-1 / var / lib / mobyle / programs / netchop.xml

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<?xml version='1.0' encoding='UTF-8'?>
<!-- XML Authors: Corinne Maufrais, Nicolas Joly and Bertrand Neron,             -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris.         -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
  <head>
    <name>netchop</name>
    <version>3.1</version>
    <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/cbs_package.xml"/>
    <doc>
      <title>netChop</title>
      <description>
        <text lang="en">predict cleavage sites for human proteasome.</text>
      </description>
      <sourcelink>http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netchop</sourcelink>
      <authors>Morten Nielsen, mniel@cbs.dtu.dk</authors>
      <reference>The role of the proteasome in generating cytotoxic T cell epitopes:
                 Insights obtained from improved predictions of proteasomal cleavage.
                 M. Nielsen, C. Lundegaard, S. Brunak, O. Lund, and C. Kesmir.
                 Immunogenetics., 57(1-2):33-41, 2005.
      </reference>
      <doclink>http://www.cbs.dtu.dk/services/NetChop/</doclink>
    </doc>
    <category>sequence:protein:motifs</category>
    <category>sequence:protein:pattern</category>
    <category>sequence:protein:profiles</category>
  </head>
  <parameters>
     
    <parameter ishidden="1" iscommand="1">
      <name>netchop</name>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">"netChop "</code>
        <code proglang="python">"netChop "</code>
      </format>
    </parameter>
   
    <parameter ismandatory="1" issimple="1" ismaininput="1">
      <name>sequence</name>
      <prompt lang="en">Input Sequence</prompt>
      <type>
        <datatype>
          <class>Sequence</class>
        </datatype>
        <dataFormat>FASTA</dataFormat>
      </type>
      <format>
        <code proglang="perl">" $value"</code>
        <code proglang="python">" " + str( value )</code>
      </format>
      <argpos>50</argpos>
      <example>
&gt;gi|33331470|gb|AAQ10915.1|     55      ISERILSTY       A1
MAGRSGDNDEELLKAVRIIKILYKSNPYPEPKGSRQARKNRRRRWRARQRQIDSISERILSTYL
GRSTEPVPLQLPPLERLHLDCREDCGTSGTQQSQGVETGVGRPQISVESPVILGSRTKN
      </example>
    </parameter>
    
    <parameter >
      <name>Method</name>
      <prompt lang="en">Prediction method (-v).</prompt>
      <type>
        <datatype>
          <class>Choice</class>
        </datatype>
      </type>
      <vdef>
        <value>0</value>
      </vdef>
      <vlist>
        <velem>
          <value>0</value>
          <label>Cterm-3.0</label>
        </velem>
        <velem>
          <value>1</value>
          <label>20S-3.0</label>
        </velem>
      </vlist>
      <format>
        <code proglang="perl">(defined $value and $value ne $vdef)? " -v $value": ""</code>
        <code proglang="python">( "" , " -v "+ value )[ value is not None and value != vdef ]</code>
      </format>
      <argpos>10</argpos>
      <comment>
       <text lang="en">
       netchop has  been  trained using  a  novel  sequence  encoding scheme, 
       and an improved neural network training strategy. 
       The netchop 3.0 version has two different network  methods  that  can  be
       used for prediction.  Cterm-3.0 and 20S-3.0.
       
       </text>
      </comment>
    </parameter>  

    <parameter>
      <name>threshold</name>
      <prompt lang="en">Use value as threshold for cleavage sites (-t).</prompt>
      <type>
        <datatype>
          <class>Float</class>
        </datatype>
      </type>
      <vdef>
        <value>0.5</value>
      </vdef>
      <format>
        <code proglang="perl">(defined $value and $value ne $vdef)? " -t $value": ""</code>
        <code proglang="python">( "" , " -t "+str(value) )[value is not None and value != vdef]</code>
      </format>
      <argpos>20</argpos>
    </parameter>
    
        <parameter>
      <name>short_output</name>
      <prompt lang="en">Use short format for output (-s).</prompt>
      <type>
        <datatype>
          <class>Boolean</class>
        </datatype>
      </type>
      <vdef>
        <value>0</value>
      </vdef>
      <format>
        <code proglang="perl">($value)? " -s": ""</code>
        <code proglang="python">( ""," -s ")[ bool( value ) ]</code>
      </format>
      <argpos>30</argpos>
    </parameter>

    <parameter isstdout="1">
      <name>results</name>
      <prompt lang="en">netChop report.</prompt>
      <type>
        <datatype>
          <superclass>Report</superclass>
          <class>NetChop</class>
        </datatype>
      </type>
      <filenames>
        <code proglang="perl">"netchop.out"</code>
        <code proglang="python">"netchop.out"</code>
      </filenames>
    </parameter> 

  </parameters>
</program>

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