/var/lib/mobyle/programs/primo.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 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>primo</name>
<doc>
<title>PRIMO</title>
<description>
<text lang="en">A primer design tool</text>
</description>
<authors>Kupfer, Li</authors>
<reference>P. Li, K. C. Kupfer, C. J. Davies, D. Burbee, G. A. Evans, and H. R. Garner. PRIMO: A primer design program that applies base quality statistics for automated large-scale DNA sequencing. Genomics 40:476-485 (1997).</reference>
</doc>
<category>sequence:nucleic:primers</category>
<command>primo</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>input_file_name</name>
<prompt lang="en">Sequence data</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" "+str(value)</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter ishidden="1">
<name>all</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">" -all"</code>
<code proglang="python">" -all"</code>
</format>
<argpos>10</argpos>
</parameter>
<parameter>
<name>cover</name>
<prompt lang="en">Cover template with walking-primers on both strands (-cover)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -cover" : ""</code>
<code proglang="python">( "" , " -cover" )[ value ]</code>
</format>
<argpos>10</argpos>
</parameter>
<parameter>
<name>print</name>
<prompt lang="en">Print formatted/annotated sequence to log file (-print)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $cover</code>
<code proglang="python">not cover</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -print" : ""</code>
<code proglang="python">( "" , " -print" )[ value ]</code>
</format>
<argpos>10</argpos>
</parameter>
<parameter>
<name>regions_file</name>
<prompt lang="en">Regions file (-read)</prompt>
<type>
<datatype>
<class>PrimoRegion</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -read $value" : ""</code>
<code proglang="python">( "" , " -read " + str(value) )[ value is not None ]</code>
</format>
<argpos>10</argpos>
</parameter>
<parameter>
<name>qual_file</name>
<prompt lang="en">Use quality data? (-noqual)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? "" : " -noqual"</code>
<code proglang="python">( " -noqual" , "" )[ value ]</code>
</format>
<argpos>10</argpos>
</parameter>
<parameter>
<name>repeats_file</name>
<prompt lang="en">Repeats file</prompt>
<type>
<datatype>
<class>PrimoRepeats</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl"> (defined $value)? "ln -s $value human.rep; " : ""</code>
<code proglang="python">( "" , "ln -s " +str(value)+ " human.rep; " )[ value is not None ]</code>
</format>
<argpos>-10</argpos>
</parameter>
<parameter>
<name>oligo_file</name>
<prompt lang="en">Oligo file</prompt>
<type>
<datatype>
<class>PrimoOligo</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl"> (defined $value )? "ln -s $value oligo.screen; " : ""</code>
<code proglang="python">( "" , "ln -s " +str(value)+ " oligo.screen; " )[ value is not None ]</code>
</format>
<argpos>-10</argpos>
</parameter>
<parameter ishidden="1">
<name>rf</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $regions_file</code>
<code proglang="python">regions_file is not None</code>
</precond>
<format>
<code proglang="perl">"ln -s $regions_file $input_file_name.regions && "</code>
<code proglang="python">"ln -s "+str(regions_file) + " " + str(input_file_name) + ".regions && "</code>
</format>
<argpos>-10</argpos>
</parameter>
<parameter ishidden="1">
<name>qf</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">$qual_file</code>
<code proglang="python">qual_file</code>
</precond>
<format>
<code proglang="perl">"ln -s $qual_file $input_file_name.qual; "</code>
<code proglang="python">"ln -s "+str(qual_file) + " " + str(input_file_name) + ".qual && "</code>
</format>
<argpos>-10</argpos>
</parameter>
<parameter isout="1">
<name>results_files</name>
<prompt lang="en">Output files</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"*.log"</code>
<code proglang="perl">"*.primers"</code>
<code proglang="perl">"oligo.cri"</code>
<code proglang="python">"*.log"</code>
<code proglang="python">"*.primers"</code>
<code proglang="python">"oligo.cri"</code>
</filenames>
</parameter>
</parameters>
</program>
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