mobyle-programs 5.1.1-1 / var / lib / mobyle / programs / patmatdb.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>patmatdb</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>patmatdb</title>
      <description>
        <text lang="en">Searches protein sequences with a sequence motif</text>
      </description>
      <doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/patmatdb.html</doclink>
      <doclink>http://emboss.sourceforge.net/docs/themes</doclink>
    </doc>
    <category>sequence:protein:motifs</category>
    <command>patmatdb</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>
            <biotype>Protein</biotype>
            <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_motif</name>
          <prompt lang="en">Protein motif to search for</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <format>
            <code proglang="python">("", " -motif=" + str(value))[value is not None]</code>
          </format>
          <argpos>2</argpos>
          <comment>
            <text lang="en">Patterns for patmatdb are based on the format of pattern used in the PROSITE database. For example:  '[DE](2)HS{P}X(2)PX(2,4)C' means two Asps or Glus in any order  followed by His, Ser, any residue other then Pro, then two of any  residue followed by Pro followed by two to four of any residue  followed by Cys. The search is case-independent, so 'AAA' matches  'aaa'.</text>
          </comment>
        </parameter>
      </parameters>
    </paragraph>

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

      <parameters>

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

        <parameter>
          <name>e_rformat_outfile</name>
          <prompt lang="en">Choose the report output format</prompt>
          <type>
            <datatype>
              <class>Choice</class>
            </datatype>
          </type>
          <vdef>
            <value>DBMOTIF</value>
          </vdef>
          <vlist>
            <velem>
              <value>DASGFF</value>
              <label>Dasgff</label>
            </velem>
            <velem>
              <value>DBMOTIF</value>
              <label>Dbmotif</label>
            </velem>
            <velem>
              <value>DIFFSEQ</value>
              <label>Diffseq</label>
            </velem>
            <velem>
              <value>EMBL</value>
              <label>Embl</label>
            </velem>
            <velem>
              <value>EXCEL</value>
              <label>Excel</label>
            </velem>
            <velem>
              <value>FEATTABLE</value>
              <label>Feattable</label>
            </velem>
            <velem>
              <value>GENBANK</value>
              <label>Genbank</label>
            </velem>
            <velem>
              <value>GFF</value>
              <label>Gff</label>
            </velem>
            <velem>
              <value>LISTFILE</value>
              <label>Listfile</label>
            </velem>
            <velem>
              <value>MOTIF</value>
              <label>Motif</label>
            </velem>
            <velem>
              <value>NAMETABLE</value>
              <label>Nametable</label>
            </velem>
            <velem>
              <value>CODATA</value>
              <label>Codata</label>
            </velem>
            <velem>
              <value>REGIONS</value>
              <label>Regions</label>
            </velem>
            <velem>
              <value>SEQTABLE</value>
              <label>Seqtable</label>
            </velem>
            <velem>
              <value>SIMPLE</value>
              <label>Simple</label>
            </velem>
            <velem>
              <value>SRS</value>
              <label>Srs</label>
            </velem>
            <velem>
              <value>SWISS</value>
              <label>Swiss</label>
            </velem>
            <velem>
              <value>TABLE</value>
              <label>Table</label>
            </velem>
            <velem>
              <value>TAGSEQ</value>
              <label>Tagseq</label>
            </velem>
          </vlist>
          <format>
            <code proglang="python">("", " -rformat=" + str(value))[value is not None and value!=vdef]</code>
          </format>
          <argpos>4</argpos>
        </parameter>

        <parameter isout="1">
          <name>e_outfile_out</name>
          <prompt lang="en">outfile_out option</prompt>
          <type>
            <datatype>
              <class>Text</class>
            </datatype>
            <dataFormat>
              <ref param="e_rformat_outfile">
              </ref>
            </dataFormat>
          </type>
          <precond>
            <code proglang="python">e_rformat_outfile in ['DASGFF', 'DBMOTIF', 'DIFFSEQ', 'EMBL', 'EXCEL', 'FEATTABLE', 'GENBANK', 'GFF', 'LISTFILE', 'MOTIF', 'NAMETABLE', 'CODATA', 'REGIONS', 'SEQTABLE', 'SIMPLE', 'SRS', 'SWISS', 'TABLE', 'TAGSEQ']</code>
          </precond>
          <filenames>
            <code proglang="python">e_outfile</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>5</argpos>
    </parameter>
  </parameters>
</program>

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