/var/lib/mobyle/programs/squizz_checker.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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 | <?xml version='1.0' encoding='UTF-8'?>
<!-- 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>squizz_checker</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/squizz_package.xml"/>
<version>0.99b</version>
<doc>
<title>SQUIZZ</title>
<description>
<text lang="en">Sequence/Alignment format checker</text>
</description>
<authors>N. Joly</authors>
<doclink>http://bioweb2.pasteur.fr/docs/squizz/seqfmt.html</doclink>
<doclink>http://bioweb2.pasteur.fr/docs/squizz/alifmt.html</doclink>
</doc>
<category>alignment:formatter</category>
<category>sequence:formatter</category>
<command>squizz</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>infile</name>
<prompt lang="en">Sequence/Alignment</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" "+str(value)</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter>
<name>strict</name>
<prompt lang="en">Disable strict format checks (-s)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -s" : ""</code>
<code proglang="python">("", " -s")[value is not None and value !=vdef]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Enabled by default</text>
</comment>
</parameter>
</parameters>
</program>
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