/var/lib/mobyle/programs/hmmconvert.xml is in mobyle-programs 5.1.2-1.
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 -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>hmmconvert</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/hmmer_package.xml"/>
<doc>
<title>HMMCONVERT</title>
<description>
<text lang="en">Convert profile HMM file to a HMMER format</text>
</description>
<comment>
<text lang="en">hmmconvert reads an HMM file from oldhmmfile in any HMMER format, and writes it to a new file newhmmfile in a new format. oldhmmfile and newhmmfile must be different files; you can't reliably overwrite the old file. By default, the new HMM file is written in HMMER 2 ASCII format.</text>
</comment>
</doc>
<category>hmm:building</category>
<command>hmmconvert</command>
</head>
<parameters>
<parameter>
<name>oldhmmfile</name>
<prompt lang="en">Old HMM ascii file</prompt>
<type>
<datatype>
<class>HmmProfile</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">not $oldhmmfile </code>
<code proglang="python">oldhmmfile is not None</code>
</precond>
<format>
<code proglang="perl">" $oldhmmfile"</code>
<code proglang="python">" " + str(oldhmmfile)</code>
</format>
<ctrl>
<message>
<text lang="en">Do not enter ascii and bin files at the same time</text>
</message>
<code proglang="perl">not defined $oldbinfile</code>
<code proglang="python">oldbinfile is None</code>
</ctrl>
<argpos>2</argpos>
</parameter>
<parameter>
<name>oldbinfile</name>
<prompt lang="en">Old HMM binary file</prompt>
<type>
<datatype>
<class>HmmProfileBin</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">not $oldhmmfile </code>
<code proglang="python">oldbinfile is not None</code>
</precond>
<format>
<code proglang="perl">" $oldbinfile"</code>
<code proglang="python">" " + str(oldbinfile)</code>
</format>
<ctrl>
<message>
<text lang="en">Do not enter ascii and bin files at the same time</text>
</message>
<code proglang="perl">not defined $oldhmmfile</code>
<code proglang="python">oldhmmfile is None</code>
</ctrl>
<argpos>2</argpos>
</parameter>
<paragraph>
<name>advanced</name>
<prompt lang="en">Advanced options</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>new_format</name>
<prompt lang="en">New format</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>-a</value>
</vdef>
<vlist>
<velem>
<value>-a</value>
<label>HMMER to ASCII file</label>
</velem>
<velem>
<value>-b</value>
<label>HMMER to binary file</label>
</velem>
<velem>
<value>-2</value>
<label>output backward compatible HMMER2 ASCII format</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value)? " $value":""</code>
<code proglang="python">" "+str(value)</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>outfmt</name>
<prompt lang="en">Choose output legacy 3.x file formats by name</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$new_format ne '-2'</code>
<code proglang="python">new_format != '-2'</code>
</precond>
<vdef>
<value>3/b</value>
</vdef>
<vlist>
<velem>
<value>3/b</value>
<label>3/b code</label>
</velem>
<velem>
<value>3/a</value>
<label>3/a code</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value ne $vdef)? " --outfmt $value":""</code>
<code proglang="python">("", " --outfmt "+str(value))[value !=vdef]</code>
</format>
<comment>
<text lang="en">Output in a HMMER3 ASCII text format other then the most current one. Valid
choices for the value are '3/b' or '3/a'. The current format is '3/b', and this is the
default. There is a slightly different format '3/a' that was used in some alpha test
code.</text>
</comment>
<argpos>1</argpos>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>result_file</name>
<prompt lang="en">Hmm profile</prompt>
<type>
<datatype>
<class>HmmProfile</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$new_format eq '-a' or $new_format eq '-2'</code>
<code proglang="python">new_format == '-a' or new_format == '-2'</code>
</precond>
<format>
<code proglang="perl">(defined $oldhmmfile)? "> $oldhmmfile.convert": "> $oldbinfile.convert"</code>
<code proglang="python">("> " + str(oldbinfile) + ".convert", "> " + str(oldhmmfile) + ".convert")[oldhmmfile is not None]</code>
</format>
<argpos>3</argpos>
<filenames>
<code proglang="perl">(defined $oldhmmfile)? "$oldhmmfile.convert": "$oldbinfile.convert"</code>
<code proglang="python">(str(oldbinfile) + ".convert" , str(oldhmmfile) + ".convert")[oldhmmfile is not None]</code>
</filenames>
</parameter>
<parameter isout="1">
<name>result_bin_file</name>
<prompt lang="en">Hmm profile (binary)</prompt>
<type>
<datatype>
<class>HmmProfileBin</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$new_format eq '-b'</code>
<code proglang="python">new_format == '-b'</code>
</precond>
<format>
<code proglang="perl">(defined $oldhmmfile)? "> $oldhmmfile.bin": "> $oldbinfile.bin"</code>
<code proglang="python">("> " + str(oldbinfile) + ".bin", "> " + str(oldhmmfile) + ".bin")[oldhmmfile is not None]</code>
</format>
<argpos>3</argpos>
<filenames>
<code proglang="perl">(defined $oldhmmfile)? "$oldhmmfile.bin":"oldbinfile.bin"</code>
<code proglang="python">(str(oldbinfile) + ".bin" , str(oldhmmfile) + ".bin")[oldhmmfile is not None]</code>
</filenames>
</parameter>
</parameters>
</program>
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