File: notseq.xml

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<?xml version="1.0" encoding="ISO-8859-1"?>

<!-- XML Authors: Corinne Maufrais and Nicolas Joly,                             -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris.         -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->

<program>
  <head>
    <name>notseq</name>
    <package>
      <name>EMBOSS</name>
      <version>6.3.1</version>
      <doc>
        <title>EMBOSS</title>
        <description>
          <text lang="en">European Molecular Biology Open Software Suite</text>
        </description>
        <authors>Rice,P. Longden,I. and Bleasby, A.</authors>
        <reference>EMBOSS: The European Molecular Biology Open Software Suite (2000)  Rice,P. Longden,I. and Bleasby, A. Trends in Genetics 16, (6) pp276--277</reference>
        <sourcelink>http://emboss.sourceforge.net/download</sourcelink>
        <homepagelink>http://emboss.sourceforge.net</homepagelink>
      </doc>
    </package>
    <doc>
      <title>notseq</title>
      <description>
        <text lang="en">Write to file a subset of an input stream of sequences</text>
      </description>
      <doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/notseq.html</doclink>
      <doclink>http://emboss.sourceforge.net/docs/themes</doclink>
    </doc>
    <category>sequence:edit</category>
    <command>notseq</command>
  </head>

  <parameters>

    <paragraph>
      <name>e_input</name>
      <prompt lang="en">Input section</prompt>

      <parameters>

        <parameter issimple="1" ismandatory="1">
          <name>e_sequence</name>
          <prompt lang="en">sequence option</prompt>
          <type>
            <datatype>
              <class>Sequence</class>
            </datatype>
            <dataFormat>EMBL</dataFormat>
            <dataFormat>FASTA</dataFormat>
            <dataFormat>GCG</dataFormat>
            <dataFormat>GENBANK</dataFormat>
            <dataFormat>NBRF</dataFormat>
            <dataFormat>CODATA</dataFormat>
            <dataFormat>RAW</dataFormat>
            <dataFormat>SWISSPROT</dataFormat>
            <dataFormat>GFF</dataFormat>
            <card>1,n</card>
          </type>
          <format>
            <code proglang="python">("", " -sequence=" + str(value))[value is not None]</code>
          </format>
          <argpos>1</argpos>
        </parameter>
      </parameters>
    </paragraph>

    <paragraph>
      <name>e_required</name>
      <prompt lang="en">Required section</prompt>

      <parameters>

        <parameter issimple="1" ismandatory="1">
          <name>e_exclude</name>
          <prompt lang="en">Sequence names to exclude</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <format>
            <code proglang="python">("", " -exclude=" + str(value))[value is not None]</code>
          </format>
          <argpos>2</argpos>
          <comment>
            <text lang="en">Enter a list of sequence names or accession numbers to exclude from the sequences read in. The excluded sequences will be  written to the file specified in the 'junkout' parameter. The  remainder will be written out to the file specified in the  'outseq' parameter. 
  The list of sequence names can be separated by either spaces or  commas. 
  The sequence names can be wildcarded. 
  The sequence names are case independent. 
  An example of a list of sequences to be excluded is: 
  myseq, hs*, one two three 
  a file containing a list of sequence names can be specified by  giving the file name preceeded by a '@', eg: '@names.dat'</text>
          </comment>
        </parameter>
      </parameters>
    </paragraph>

    <paragraph>
      <name>e_output</name>
      <prompt lang="en">Output section</prompt>

      <parameters>

        <parameter>
          <name>e_outseq</name>
          <prompt lang="en">Name of the output sequence file (e_outseq)</prompt>
          <type>
            <datatype>
              <class>Filename</class>
            </datatype>
          </type>
          <vdef>
            <value>notseq.e_outseq</value>
          </vdef>
          <format>
            <code proglang="python">("" , " -outseq=" + str(value))[value is not None]</code>
          </format>
          <argpos>3</argpos>
        </parameter>

        <parameter>
          <name>e_osformat_outseq</name>
          <prompt lang="en">Choose the sequence output format</prompt>
          <type>
            <datatype>
              <class>Choice</class>
            </datatype>
          </type>
          <vdef>
            <value>FASTA</value>
          </vdef>
          <vlist>
            <velem>
              <value>EMBL</value>
              <label>Embl</label>
            </velem>
            <velem>
              <value>FASTA</value>
              <label>Fasta</label>
            </velem>
            <velem>
              <value>GCG</value>
              <label>Gcg</label>
            </velem>
            <velem>
              <value>GENBANK</value>
              <label>Genbank</label>
            </velem>
            <velem>
              <value>NBRF</value>
              <label>Nbrf</label>
            </velem>
            <velem>
              <value>CODATA</value>
              <label>Codata</label>
            </velem>
            <velem>
              <value>RAW</value>
              <label>Raw</label>
            </velem>
            <velem>
              <value>SWISSPROT</value>
              <label>Swissprot</label>
            </velem>
            <velem>
              <value>GFF</value>
              <label>Gff</label>
            </velem>
          </vlist>
          <format>
            <code proglang="python">("", " -osformat=" + str(value))[value is not None and value!=vdef]</code>
          </format>
          <argpos>4</argpos>
        </parameter>

        <parameter isout="1">
          <name>e_outseq_out</name>
          <prompt lang="en">outseq_out option</prompt>
          <type>
            <datatype>
              <class>Sequence</class>
            </datatype>
            <dataFormat>
              <ref param="e_osformat_outseq">
              </ref>
            </dataFormat>
          </type>
          <filenames>
            <code proglang="python">e_outseq</code>
          </filenames>
        </parameter>

        <parameter>
          <name>e_junkoutseq</name>
          <prompt lang="en">Name of the output sequence file (e_junkoutseq)</prompt>
          <type>
            <datatype>
              <class>Filename</class>
            </datatype>
          </type>
          <vdef>
            <value>notseq.e_junkoutseq</value>
          </vdef>
          <format>
            <code proglang="python">("" , " -junkoutseq=" + str(value))[value is not None]</code>
          </format>
          <argpos>5</argpos>
          <comment>
            <text lang="en">This file collects the sequences which you have excluded from the main output file of sequences.</text>
          </comment>
        </parameter>

        <parameter>
          <name>e_osformat_junkoutseq</name>
          <prompt lang="en">Choose the sequence output format</prompt>
          <type>
            <datatype>
              <class>Choice</class>
            </datatype>
          </type>
          <vdef>
            <value>FASTA</value>
          </vdef>
          <vlist>
            <velem>
              <value>EMBL</value>
              <label>Embl</label>
            </velem>
            <velem>
              <value>FASTA</value>
              <label>Fasta</label>
            </velem>
            <velem>
              <value>GCG</value>
              <label>Gcg</label>
            </velem>
            <velem>
              <value>GENBANK</value>
              <label>Genbank</label>
            </velem>
            <velem>
              <value>NBRF</value>
              <label>Nbrf</label>
            </velem>
            <velem>
              <value>CODATA</value>
              <label>Codata</label>
            </velem>
            <velem>
              <value>RAW</value>
              <label>Raw</label>
            </velem>
            <velem>
              <value>SWISSPROT</value>
              <label>Swissprot</label>
            </velem>
            <velem>
              <value>GFF</value>
              <label>Gff</label>
            </velem>
          </vlist>
          <format>
            <code proglang="python">("", " -osformat=" + str(value))[value is not None and value!=vdef]</code>
          </format>
          <argpos>6</argpos>
        </parameter>

        <parameter isout="1">
          <name>e_junkoutseq_out</name>
          <prompt lang="en">junkoutseq_out option</prompt>
          <type>
            <datatype>
              <class>Sequence</class>
            </datatype>
            <dataFormat>
              <ref param="e_osformat_junkoutseq">
              </ref>
            </dataFormat>
          </type>
          <filenames>
            <code proglang="python">e_junkoutseq</code>
          </filenames>
        </parameter>
      </parameters>
    </paragraph>

    <parameter ishidden="1">
      <name>auto</name>
      <prompt lang="en">Turn off any prompting</prompt>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <format>
        <code proglang="python">" -auto -stdout"</code>
      </format>
      <argpos>7</argpos>
    </parameter>
  </parameters>
</program>