/var/lib/mobyle/programs/compseq.xml is in mobyle-programs 5.1.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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<!-- 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>compseq</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>compseq</title>
<description>
<text lang="en">Calculate the composition of unique words in sequences</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/compseq.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>sequence:nucleic:composition</category>
<category>sequence:protein:composition</category>
<command>compseq</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>
<parameter>
<name>e_infile</name>
<prompt lang="en">Program compseq output file (optional)</prompt>
<type>
<datatype>
<class>CompseqReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<format>
<code proglang="python">("", " -infile=" + str(value))[value is not None]</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">This is a file previously produced by 'compseq' that can be used to set the expected frequencies of words in this analysis.
The word size in the current run must be the same as the one in this results file. Obviously, you should use a file produced from protein sequences if you are counting protein sequence word frequencies, and you must use one made from nucleotide frequencies if you are analysing a nucleotide sequence.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_required</name>
<prompt lang="en">Required section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_word</name>
<prompt lang="en">Word size to consider (e.g. 2=dimer) (value greater than or equal to 1)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>2</value>
</vdef>
<format>
<code proglang="python">("", " -word=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 1 is required</text>
</message>
<code proglang="python">value >= 1</code>
</ctrl>
<argpos>3</argpos>
<comment>
<text lang="en">This is the size of word (n-mer) to count.
Thus if you want to count codon frequencies for a nucleotide sequence, you should enter 3 here.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_additional</name>
<prompt lang="en">Additional section</prompt>
<parameters>
<parameter>
<name>e_frame</name>
<prompt lang="en">Frame of word to look at (0=all frames) (value greater than or equal to 0)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -frame=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 0 is required</text>
</message>
<code proglang="python">value >= 0</code>
</ctrl>
<argpos>4</argpos>
<comment>
<text lang="en">The normal behaviour of 'compseq' is to count the frequencies of all words that occur by moving a window of length 'word' up by one each time.
This option allows you to move the window up by the length of the word each time, skipping over the intervening words.
You can count only those words that occur in a single frame of the word by setting this value to a number other than zero.
If you set it to 1 it will only count the words in frame 1, 2 will only count the words in frame 2 and so on.</text>
</comment>
</parameter>
<parameter>
<name>e_ignorebz</name>
<prompt lang="en">Ignore the amino acids b and z and just count them as 'other'</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noignorebz", "")[ bool(value) ]</code>
</format>
<argpos>5</argpos>
<comment>
<text lang="en">The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid.
These are not commonly used codes and you may wish not to count words containing them, just noting them in the count of 'Other' words.</text>
</comment>
</parameter>
<parameter>
<name>e_reverse</name>
<prompt lang="en">Count words in the forward and reverse sense</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -reverse")[ bool(value) ]</code>
</format>
<argpos>6</argpos>
<comment>
<text lang="en">Set this to be true if you also wish to also count words in the reverse complement of a nucleic sequence.</text>
</comment>
</parameter>
<parameter>
<name>e_calcfreq</name>
<prompt lang="en">Calculate expected frequency from sequence</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -calcfreq")[ bool(value) ]</code>
</format>
<argpos>7</argpos>
<comment>
<text lang="en">If this is set true then the expected frequencies of words are calculated from the observed frequency of single bases or residues in the sequences.
If you are reporting a word size of 1 (single bases or residues) then there is no point in using this option because the calculated expected frequency will be equal to the observed frequency.
Calculating the expected frequencies like this will give an approximation of the expected frequencies that you might get by using an input file of frequencies produced by a previous run of this program. If an input file of expected word frequencies has been specified then the values from that file will be used instead of this calculation of expected frequency from the sequence, even if 'calcfreq' is set to be true.</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 output file (e_outfile)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>outfile.composition</value>
</vdef>
<format>
<code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
</format>
<argpos>8</argpos>
<comment>
<text lang="en">This is the results file.</text>
</comment>
</parameter>
<parameter isout="1">
<name>e_outfile_out</name>
<prompt lang="en">outfile_out option</prompt>
<type>
<datatype>
<class>CompseqReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="python">e_outfile</code>
</filenames>
</parameter>
<parameter>
<name>e_zerocount</name>
<prompt lang="en">Display the words that have a frequency of zero</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nozerocount", "")[ bool(value) ]</code>
</format>
<argpos>9</argpos>
<comment>
<text lang="en">You can make the output results file much smaller if you do not display the words with a zero count.</text>
</comment>
</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>10</argpos>
</parameter>
</parameters>
</program>
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