/var/lib/mobyle/programs/golden.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, 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>golden</name>
<version>1.1a</version>
<doc>
<title>GOLDEN</title>
<description>
<text lang="en">Fetch a database entry</text>
</description>
<authors>N. Joly</authors>
<sourcelink>ftp://ftp.pasteur.fr/pub/gensoft/projects/golden/</sourcelink>
</doc>
<category>database:search:sequence</category>
<command>golden</command>
</head>
<parameters xmlns:xi="http://www.w3.org/2001/XInclude">
<parameter ismandatory="1" issimple="1" ismaininput="1">
<name>db</name>
<prompt lang="en">Database</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<xi:include href="../../Local/Services/Programs/Env/goldendb.xml" />
<format>
<code proglang="perl">" $db:"</code>
<code proglang="python">" " + db + ":"</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter ismandatory="1" issimple="1" ismaininput="1">
<name>query</name>
<prompt lang="en">Query (Entry name or Accession number)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"$value"</code>
<code proglang="python">str(value)</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter>
<name>ac</name>
<prompt lang="en">Search with Accession number only (-a)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -a" : ""</code>
<code proglang="python">( "" , " -a" )[ value ]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>Id</name>
<prompt lang="en">Search with entry name only (-i)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -i" : ""</code>
<code proglang="python">( "" , " -i" )[ value ]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter isstdout="1">
<name>nucleic_sequence_out</name>
<prompt lang="en">Sequence</prompt>
<precond>
<code proglang="perl">$db =~ /^(embl|genbank|imgt|rdpii)$/</code>
<code proglang="python">db in ( 'embl' , 'genbank' , 'imgt' ,'rdpii' )</code>
</precond>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>
<test param="db" eq="embl">EMBL</test>
<test param="db" eq="genbank">GENBANK</test>
<test param="db" eq="imgt">EMBL</test>
<test param="db" eq="rdpii">GENBANK</test>
<test param="db" eq="refseq">GENBANK</test>
</dataFormat>
</type>
<filenames>
<code proglang="perl">"golden.out"</code>
<code proglang="python">"golden.out"</code>
</filenames>
</parameter>
<parameter isstdout="1">
<name>protein_sequence_out</name>
<prompt lang="en">Sequence</prompt>
<precond>
<code proglang="perl">$db =~ /^(genpept|uniprot)$/</code>
<code proglang="python">db in ( 'genpept' , 'uniprot' )</code>
</precond>
<type>
<biotype>Protein</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>
<test param="db" eq="genpept">GENBANK</test>
<test param="db" eq="uniprot">SWISSPROT</test>
</dataFormat>
</type>
<filenames>
<code proglang="perl">"golden.out"</code>
<code proglang="python">"golden.out"</code>
</filenames>
</parameter>
<parameter isstdout="1">
<name>refseq_out</name>
<prompt lang="en">Sequence</prompt>
<precond>
<code proglang="perl">$db eq 'refseq'</code>
<code proglang="python">db == 'refseq' </code>
</precond>
<type>
<biotype>DNA</biotype>
<biotype>Protein</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>GENBANK</dataFormat>
</type>
<filenames>
<code proglang="perl">"golden.out"</code>
<code proglang="python">"golden.out"</code>
</filenames>
</parameter>
<parameter isstdout="1">
<name>motif_out</name>
<prompt lang="en">Motif</prompt>
<precond>
<code proglang="perl">$db eq 'prosite'</code>
<code proglang="python">db == 'prosite'</code>
</precond>
<type>
<biotype>Protein</biotype>
<datatype>
<superclass>AbstractText</superclass>
<class>Motif</class>
</datatype>
<dataFormat>PROSITE</dataFormat>
</type>
<filenames>
<code proglang="perl">"golden.out"</code>
<code proglang="python">"golden.out"</code>
</filenames>
</parameter>
<parameter isstdout="1">
<name>enzyme_out</name>
<prompt lang="en">Enzyme</prompt>
<precond>
<code proglang="perl">$db eq 'enzyme'</code>
<code proglang="python">db == 'enzyme'</code>
</precond>
<type>
<biotype>Protein</biotype>
<datatype>
<superclass>AbstractText</superclass>
<class>Enzyme</class>
</datatype>
<dataFormat>ENZYME</dataFormat>
</type>
<filenames>
<code proglang="perl">"golden.out"</code>
<code proglang="python">"golden.out"</code>
</filenames>
</parameter>
</parameters>
</program>
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