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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>digest</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>digest</title>
      <description>
        <text lang="en">Reports on protein proteolytic enzyme or reagent cleavage sites</text>
      </description>
      <doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/digest.html</doclink>
      <doclink>http://emboss.sourceforge.net/docs/themes</doclink>
    </doc>
    <category>sequence:protein:motifs</category>
    <command>digest</command>
  </head>

  <parameters>

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

      <parameters>

        <parameter issimple="1" ismandatory="1">
          <name>e_seqall</name>
          <prompt lang="en">seqall 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">("", " -seqall=" + str(value))[value is not None]</code>
          </format>
          <argpos>1</argpos>
        </parameter>

        <parameter>
          <name>e_mwdata</name>
          <prompt lang="en">Molecular weights data file</prompt>
          <type>
            <datatype>
              <class>MolecularWeights</class>
              <superclass>AbstractText</superclass>
            </datatype>
          </type>
          <format>
            <code proglang="python">("", " -mwdata=" + str(value))[value is not None ]</code>
          </format>
          <argpos>2</argpos>
          <comment>
            <text lang="en">Molecular weight data for amino acids</text>
          </comment>
        </parameter>
      </parameters>
    </paragraph>

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

      <parameters>

        <parameter issimple="1" ismandatory="1">
          <name>e_menu</name>
          <prompt lang="en">Enzymes and reagents</prompt>
          <type>
            <datatype>
              <class>Choice</class>
            </datatype>
          </type>
          <vdef>
            <value>1</value>
          </vdef>
          <vlist>
            <velem>
              <value>1</value>
              <label>Trypsin</label>
            </velem>
            <velem>
              <value>2</value>
              <label>Lys-c</label>
            </velem>
            <velem>
              <value>3</value>
              <label>Arg-c</label>
            </velem>
            <velem>
              <value>4</value>
              <label>Asp-n</label>
            </velem>
            <velem>
              <value>5</value>
              <label>V8-bicarb</label>
            </velem>
            <velem>
              <value>6</value>
              <label>V8-phosph</label>
            </velem>
            <velem>
              <value>7</value>
              <label>Chymotrypsin</label>
            </velem>
            <velem>
              <value>8</value>
              <label>Cnbr</label>
            </velem>
          </vlist>
          <format>
            <code proglang="python">("", " -menu=" + str(value))[value is not None and value!=vdef]</code>
          </format>
          <argpos>3</argpos>
        </parameter>

        <parameter>
          <name>e_mono</name>
          <prompt lang="en">Use monoisotopic weights</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="python">("", " -mono")[ bool(value) ]</code>
          </format>
          <argpos>4</argpos>
        </parameter>
      </parameters>
    </paragraph>

    <paragraph>
      <name>e_advanced</name>
      <prompt lang="en">Advanced section</prompt>

      <parameters>

        <parameter>
          <name>e_unfavoured</name>
          <prompt lang="en">Allow unfavoured cuts</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="python">("", " -unfavoured")[ bool(value) ]</code>
          </format>
          <argpos>5</argpos>
          <comment>
            <text lang="en">Trypsin will not normally cut after 'KR' if they are followed by any of  'KRIFLP'. Lys-C will not normally cut  after 'K' if it is followed by 'P'.  Arg-C will not normally cut after 'R'  if it is followed by 'P'. V8-bicarb  will not normally cut after 'E' if it  is followed by any of 'KREP'.  V8-phosph will not normally cut after  'DE' if they are followed by 'P'.  Chymotrypsin will not normally cut  after 'FYWLM' if they are followed by  'P'. Specifying unfavoured shows  these unfavoured cuts as well as the  favoured ones.</text>
          </comment>
        </parameter>

        <parameter>
          <name>e_ragging</name>
          <prompt lang="en">Allow ragging</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="python">("", " -ragging")[ bool(value) ]</code>
          </format>
          <argpos>6</argpos>
          <comment>
            <text lang="en">Allows semi-specific and non-specific digestion. This option is  particularly useful for generating  lists of peptide sequences for  protein identification using  mass-spectrometry.</text>
          </comment>
        </parameter>

        <parameter>
          <name>e_termini</name>
          <prompt lang="en">Ragging value (value from 1 to 4)</prompt>
          <type>
            <datatype>
              <class>Choice</class>
            </datatype>
          </type>
          <vdef>
            <value>1</value>
          </vdef>
          <vlist>
            <velem>
              <value>1</value>
              <label>None</label>
            </velem>
            <velem>
              <value>2</value>
              <label>Nterm</label>
            </velem>
            <velem>
              <value>3</value>
              <label>Cterm</label>
            </velem>
            <velem>
              <value>4</value>
              <label>Nterm or cterm</label>
            </velem>
          </vlist>
          <format>
            <code proglang="python">("", " -termini=" + str(value))[value is not None and value!=vdef]</code>
          </format>
          <argpos>7</argpos>
        </parameter>
      </parameters>
    </paragraph>

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

      <parameters>

        <parameter>
          <name>e_overlap</name>
          <prompt lang="en">Show overlapping partials</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="python">("", " -overlap")[ bool(value) ]</code>
          </format>
          <argpos>8</argpos>
          <comment>
            <text lang="en">Used for partial digestion. Shows all cuts from favoured cut sites plus  1..3, 2..4, 3..5 etc but not (e.g.)  2..5. Overlaps are therefore  fragments with exactly one potential  cut site within it.</text>
          </comment>
        </parameter>

        <parameter>
          <name>e_allpartials</name>
          <prompt lang="en">Show all partials</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="python">("", " -allpartials")[ bool(value) ]</code>
          </format>
          <argpos>9</argpos>
          <comment>
            <text lang="en">As for overlap but fragments containing more than one potential  cut site are included.</text>
          </comment>
        </parameter>

        <parameter>
          <name>e_outfile</name>
          <prompt lang="en">Name of the report file</prompt>
          <type>
            <datatype>
              <class>Filename</class>
            </datatype>
          </type>
          <vdef>
            <value>digest.report</value>
          </vdef>
          <format>
            <code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
          </format>
          <argpos>10</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>SEQTABLE</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>11</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>12</argpos>
    </parameter>
  </parameters>
</program>