/var/lib/mobyle/programs/concatfasta.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, Nicolas Joly, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>concatfasta</name>
<version>1.0</version>
<doc>
<title>concatfasta</title>
<description>
<text lang="en">Concatenation of sequences from two fasta files with exactly the same sequence identifiers</text>
</description>
<authors>Maufrais Corinne</authors>
</doc>
<category>sequence:formatter</category>
<command>concatfasta</command>
</head>
<parameters>
<paragraph>
<name>input</name>
<prompt lang="en">Input section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>firstFile</name>
<prompt lang="en">Fasta file</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
<card>1,1</card>
</type>
<format>
<code proglang="python">("", " -f " + str(value))[value is not None]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter issimple="1" ismandatory="1">
<name>scdFile</name>
<prompt lang="en">Fasta file</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
<card>1,1</card>
</type>
<format>
<code proglang="python">("", " -s " + str(value))[value is not None]</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter isstdout="1">
<name>outfile</name>
<prompt>Sequence(s) file</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
<card>1,n</card>
</type>
<filenames>
<code proglang="perl">"concatfasta.out"</code>
<code proglang="python">"concatfasta.out"</code>
</filenames>
</parameter>
</parameters>
</paragraph>
</parameters>
</program>
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