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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>combat</name>
    <version>1.0</version>
    <doc>
      <title>COMBAT</title>
      <description>
        <text lang="en">Comparison of coding DNA</text>
      </description>
      <authors>Pedersen, Lyngso,Hein</authors>
      <reference>Christian N. S. Pedersen, Rune B. Lyngso and Jotun Hein. Comparison of coding DNA in Proceedings of the 9th Annual Symposium of Combinatorial Pattern Matching (CPM), 1998.</reference>
      <homepagelink>http://www.daimi.au.dk/~cstorm/combat/</homepagelink>
      <sourcelink>http://www.daimi.au.dk/~cstorm/combat/</sourcelink>
    </doc>
    <category>alignment:pairwise</category>
  </head>
  <parameters xmlns:xi="http://www.w3.org/2001/XInclude">
    <parameter iscommand="1" ishidden="1">
      <name>combat</name>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <precond>
        <code proglang="perl">defined $sequence1 and defined $sequence2</code>
        <code proglang="python">sequence1 is not None and sequence2 is not None</code>
      </precond>
      <format>
        <code proglang="perl">"cat $sequence1 $sequence2 &gt;&gt; sequence &amp;&amp; combat combat.params &gt;distance.out &amp;&amp; combine sequence combat.aln"</code>
        <code proglang="python">"cat " + str(sequence2) + " " + str(sequence1) + " &gt;&gt; sequence.data &amp;&amp; combat combat.params &gt; distance.out &amp;&amp; combine sequence.data combat.aln"</code>
      </format>
      <argpos>0</argpos>
    </parameter>
    <parameter ismandatory="1" issimple="1">
      <name>sequence1</name>
      <prompt lang="en">First Sequence</prompt>
      <type>
        <datatype>
          <class>Sequence</class>
        </datatype>
        <dataFormat>FASTA</dataFormat>
      </type>
      <format>
        <code proglang="perl">"&gt;inputfile\n\"sequence.data\"\n"</code>
        <code proglang="python">'&gt;inputfile\n"sequence.data"\n'</code>
      </format>
      <argpos>1</argpos>
      <comment>
        <text lang="en">Sequences must describe an integer number of codon, i.e. the length of sequence must be a multiple of three.</text>
      </comment>
      <paramfile>combat.params</paramfile>
    </parameter>
    <parameter ismandatory="1" issimple="1">
      <name>sequence2</name>
      <prompt lang="en">Second Sequence</prompt>
      <type>
        <datatype>
          <class>Sequence</class>
        </datatype>
        <dataFormat>FASTA</dataFormat>
      </type>
      <comment>
        <text lang="en">Sequences must describe an integer number of codon, i.e. the length of sequence must be a multiple of three.</text>
      </comment>
    </parameter>
    <parameter isout="1">
      <name>output_aln</name>
      <prompt lang="en">Output file</prompt>
      <type>
        <datatype>
          <class>Text</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">"&gt;outputfile\n\"combat.aln\"\n"</code>
        <code proglang="python">'&gt;outputfile\n"combat.aln"\n'</code>
      </format>
      <argpos>2</argpos>
      <paramfile>combat.params</paramfile>
      <filenames>
        <code proglang="perl">"combat.aln"</code>
        <code proglang="python">"combat.aln"</code>
      </filenames>
    </parameter>
    <parameter ismandatory="1">
      <name>protein_distance_matrix</name>
      <prompt lang="en">Amino-acid distance matrix</prompt>
      <type>
        <datatype>
          <class>Choice</class>
        </datatype>
      </type>
      <vdef>
        <value>Blosum62_distance.m</value>
      </vdef>
      <vlist>
        <velem>
          <value>PAM60_distance.m</value>
          <label>PAM60</label>
        </velem>
        <velem>
          <value>PAM120_distance.m</value>
          <label>PAM120</label>
        </velem>
        <velem>
          <value>PAM250_distance.m.m</value>
          <label>PAM250</label>
        </velem>
        <velem>
          <value>PAM350_distance.m</value>
          <label>PAM350</label>
        </velem>
        <velem>
          <value>Blosum30_distance.m</value>
          <label>Blosum30</label>
        </velem>
        <velem>
          <value>Blosum62_distance.m</value>
          <label>Blosum62</label>
        </velem>
        <velem>
          <value>Blosum90_distance.m</value>
          <label>Blosum90</label>
        </velem>
      </vlist>
      <format>
        <code proglang="perl">"&gt;distance matrix\n\"<xi:include href="../../Local/Services/Programs/Env/combat_data.xml" xpointer="xpointer(/matrix/text())" />$value\"\n"</code>
        <code proglang="python">"&gt;distance matrix\n\"<xi:include href="../../Local/Services/Programs/Env/combat_data.xml" xpointer="xpointer(/matrix/text())" />" + str(value) + '"\n'</code>
      </format>
      <argpos>3</argpos>
      <paramfile>combat.params</paramfile>
    </parameter>
    <parameter ismandatory="1">
      <name>nucleotide_distance_matrix</name>
      <prompt lang="en">Nucleotid distance matrix</prompt>
      <type>
        <datatype>
          <class>Choice</class>
        </datatype>
      </type>
      <vdef>
        <value>nucleotide_distance1.m</value>
      </vdef>
      <vlist>
        <velem>
          <value>nucleotide_distance1.m</value>
          <label>Matrix 1</label>
        </velem>
        <velem>
          <value>nucleotide_distance2.m</value>
          <label>Matrix 2</label>
        </velem>
        <velem>
          <value>nucleotide_distance3.m</value>
          <label>Matrix 3</label>
        </velem>
      </vlist>
      <format>
        <code proglang="perl">"&gt;nucleotide matrix\n\"<xi:include href="../../Local/Services/Programs/Env/combat_data.xml" xpointer="xpointer(/matrix/text())" />$value\"\n"</code>
        <code proglang="python">"&gt;nucleotide matrix\n\"<xi:include href="../../Local/Services/Programs/Env/combat_data.xml" xpointer="xpointer(/matrix/text())" />" + str(value) + '"\n'</code>
      </format>
      <argpos>4</argpos>
      <paramfile>combat.params</paramfile>
    </parameter>
    <parameter ismandatory="1" issimple="1">
      <name>protein_gap_open</name>
      <prompt lang="en">Gap open cost for protein</prompt>
      <type>
        <datatype>
          <class>Integer</class>
        </datatype>
      </type>
      <vdef>
        <value>20</value>
      </vdef>
      <format>
        <code proglang="perl">"&gt;gap functions\\nprotein:        $value"</code>
        <code proglang="python">"&gt;gap functions\nprotein:        " + str(value)</code>
      </format>
      <argpos>5</argpos>
      <paramfile>combat.params</paramfile>
    </parameter>
    <parameter ismandatory="1" issimple="1">
      <name>protein_gap_ext</name>
      <prompt lang="en">Gap extension cost for protein</prompt>
      <type>
        <datatype>
          <class>Integer</class>
        </datatype>
      </type>
      <vdef>
        <value>8</value>
      </vdef>
      <format>
        <code proglang="perl">" + $value*k\\n"</code>
        <code proglang="python">" + " + str(value) + "*k\n"</code>
      </format>
      <argpos>6</argpos>
      <paramfile>combat.params</paramfile>
    </parameter>
    <parameter ismandatory="1"  issimple="1">
      <name>dna_gap_open</name>
      <prompt lang="en">Gap open cost for dna</prompt>
      <type>
        <datatype>
          <class>Integer</class>
        </datatype>
      </type>
      <vdef>
        <value>8</value>
      </vdef>
      <format>
        <code proglang="perl">"dna:        $value"</code>
        <code proglang="python">"dna:        " + str(value)</code>
      </format>
      <argpos>7</argpos>
      <paramfile>combat.params</paramfile>
    </parameter>
    <parameter ismandatory="1" issimple="1">
      <name>dna_gap_ext</name>
      <prompt lang="en">Gap extension cost for dna</prompt>
      <type>
        <datatype>
          <class>Integer</class>
        </datatype>
      </type>
      <vdef>
        <value>2</value>
      </vdef>
      <format>
        <code proglang="perl">" + $value*k"</code>
        <code proglang="python">" + " + str(value) + "*k"</code>
      </format>
      <argpos>8</argpos>
      <paramfile>combat.params</paramfile>
    </parameter>
    <parameter isstdout="1">
      <name>combat_out</name>
      <prompt>Alignment file</prompt>
      <type>
        <datatype>
          <class>Alignment</class>
        </datatype>
        <dataFormat>FASTA</dataFormat>
      </type>
      <filenames>
        <code proglang="perl">"combat.out"</code>
        <code proglang="python">"combat.out"</code>
      </filenames>
    </parameter>
    <parameter isout="1">
      <name>distance_files</name>
      <prompt>Distance file</prompt>
      <type>
        <datatype>
          <class>Text</class>
        </datatype>
      </type>
      <filenames>
        <code proglang="perl">"distance.out"</code>
        <code proglang="python">"distance.out"</code>
      </filenames>
    </parameter>
    <parameter isout="1">
      <name>ps_files</name>
      <prompt>Postscript file</prompt>
      <type>
        <datatype>
          <class>PostScript</class>
          <superclass>Binary</superclass>
        </datatype>
      </type>
      <filenames>
        <code proglang="perl">"combat.ps"</code>
        <code proglang="python">"combat.ps"</code>
      </filenames>
    </parameter>
    <parameter ishidden="1">
      <name>gnuplot_call</name>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">" &amp;&amp; gnuplot &lt;gnuplot.params"</code>
        <code proglang="python">" &amp;&amp; gnuplot &lt;gnuplot.params"</code>
      </format>
      <argpos>100</argpos>
    </parameter>
    <parameter ishidden="1">
      <name>gnuplot_commands</name>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">"set xtics 12,5.,1000\nset ytics 12,5.,1000\nset grid\nset terminal postscript\nset output \"combat.ps\"\nplot \"combat.aln\" with lines\n"</code>
        <code proglang="python">'set xtics 12,5.,1000\nset ytics 12,5.,1000\nset grid\nset terminal postscript\nset output "combat.ps"\nplot "combat.aln" with lines\n'</code>
      </format>
      <argpos>1</argpos>
      <paramfile>gnuplot.params</paramfile>
    </parameter>
  </parameters>
</program>