/var/lib/mobyle/programs/fetchSequences.xml is in mobyle-programs 5.1.2-2.
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: Bertrand Neron -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 Licence. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>fetchSequences</name>
<version>1.0</version>
<doc>
<title>fetch sequences</title>
<description>
<text lang="en">Retrieve sequences in databases from list of identifier (USA list)</text>
</description>
<authors>EMBOSS</authors>
<reference>http://emboss.sourceforge.net/</reference>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/seqret.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>database:search:sequence</category>
<command>seqret</command>
</head>
<parameters>
<paragraph>
<name>input</name>
<prompt lang="en">Input section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>USAList</name>
<prompt lang="en">list of sequences identifier in USA format</prompt>
<type>
<datatype>
<class>GenesId</class>
<superclass>AbstractText</superclass>
</datatype>
<dataFormat>USAList</dataFormat>
<card>1</card>
</type>
<format>
<code proglang="python">" @" + str(value)</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">
list of identifiers in USA format:
databank:Acc
( one item per line )
</text>
</comment>
<example>
sp:Q74K65
sp:Q2W4W1
sp:P63394
sp:P63393
sp:P18767
sp:Q042G7
</example>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output</name>
<prompt lang="en">Output section</prompt>
<parameters>
<parameter isstdout="1">
<name>sequence_out</name>
<prompt lang="en">the sequences</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<card>(1,n)</card>
</type>
<filenames>
<code proglang="python">"fetchSequences.out"</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>10</argpos>
</parameter>
</parameters>
</program>
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