/var/lib/mobyle/programs/infoseq.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 and Nicolas Joly, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>infoseq</name>
<package>
<name>EMBOSS</name>
<version>6.3.1</version>
<doc>
<title>EMBOSS</title>
<description>
<text lang="en">European Molecular Biology Open Software Suite</text>
</description>
<authors>Rice,P. Longden,I. and Bleasby, A.</authors>
<reference>EMBOSS: The European Molecular Biology Open Software Suite (2000) Rice,P. Longden,I. and Bleasby, A. Trends in Genetics 16, (6) pp276--277</reference>
<sourcelink>http://emboss.sourceforge.net/download</sourcelink>
<homepagelink>http://emboss.sourceforge.net</homepagelink>
</doc>
</package>
<doc>
<title>infoseq</title>
<description>
<text lang="en">Display basic information about sequences</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/infoseq.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>information</category>
<command>infoseq</command>
</head>
<parameters>
<paragraph>
<name>e_input</name>
<prompt lang="en">Input section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_sequence</name>
<prompt lang="en">sequence option</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>EMBL</dataFormat>
<dataFormat>FASTA</dataFormat>
<dataFormat>GCG</dataFormat>
<dataFormat>GENBANK</dataFormat>
<dataFormat>NBRF</dataFormat>
<dataFormat>CODATA</dataFormat>
<dataFormat>RAW</dataFormat>
<dataFormat>SWISSPROT</dataFormat>
<dataFormat>GFF</dataFormat>
<card>1,n</card>
</type>
<format>
<code proglang="python">("", " -sequence=" + str(value))[value is not None]</code>
</format>
<argpos>1</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_advanced</name>
<prompt lang="en">Advanced section</prompt>
<parameters>
<parameter>
<name>e_columns</name>
<prompt lang="en">Print information in neat, aligned columns.</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nocolumns", "")[ bool(value) ]</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">Set this option on (Y) to print the sequence information into neat, aligned columns in the output file. Alternatively, leave it unset (N), in which case the information records will be delimited by a character, which you may specify by using the -delimiter option. In other words, if -columns is set on, the -delimiter option is overriden.</text>
</comment>
</parameter>
<parameter>
<name>e_delimiter</name>
<prompt lang="en">Delimiter of records in text output file</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>|</value>
</vdef>
<format>
<code proglang="python">("", " -delimiter=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">This string, which is usually a single character only, is used to delimit individual records in the text output file. It could be a space character, a tab character, a pipe character or any other character or string.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_output</name>
<prompt lang="en">Output section</prompt>
<parameters>
<parameter>
<name>e_outfile</name>
<prompt lang="en">Name of the output file (e_outfile)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>infoseq.e_outfile</value>
</vdef>
<format>
<code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
</format>
<argpos>4</argpos>
<comment>
<text lang="en">If you enter the name of a file here then this program will write the sequence details into that file.</text>
</comment>
</parameter>
<parameter isout="1">
<name>e_outfile_out</name>
<prompt lang="en">outfile_out option</prompt>
<type>
<datatype>
<class>InfoseqReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="python">e_outfile</code>
</filenames>
</parameter>
<parameter>
<name>e_html</name>
<prompt lang="en">Format output as an html table</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -html")[ bool(value) ]</code>
</format>
<argpos>5</argpos>
</parameter>
<parameter>
<name>e_only</name>
<prompt lang="en">Display the specified columns</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -only")[ bool(value) ]</code>
</format>
<argpos>6</argpos>
<comment>
<text lang="en">This is a way of shortening the command line if you only want a few things to be displayed. Instead of specifying:
'-nohead -noname -noacc -notype -nopgc -nodesc'
to get only the length output, you can specify
'-only -length'</text>
</comment>
</parameter>
<parameter>
<name>e_heading</name>
<prompt lang="en">Display column headings</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noheading", "")[ bool(value) ]</code>
</format>
<argpos>7</argpos>
</parameter>
<parameter>
<name>e_usa</name>
<prompt lang="en">Display the usa of the sequence</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="python">not e_only</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -usa")[ bool(value) ]</code>
</format>
<argpos>8</argpos>
</parameter>
<parameter>
<name>e_database</name>
<prompt lang="en">Display 'database' column</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="python">not e_only</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -database")[ bool(value) ]</code>
</format>
<argpos>9</argpos>
</parameter>
<parameter>
<name>e_name</name>
<prompt lang="en">Display 'name' column</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="python">not e_only</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -name")[ bool(value) ]</code>
</format>
<argpos>10</argpos>
</parameter>
<parameter>
<name>e_accession</name>
<prompt lang="en">Display 'accession' column</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="python">not e_only</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -accession")[ bool(value) ]</code>
</format>
<argpos>11</argpos>
</parameter>
<parameter>
<name>e_gi</name>
<prompt lang="en">Display 'gi' column</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -gi")[ bool(value) ]</code>
</format>
<argpos>12</argpos>
</parameter>
<parameter>
<name>e_seqversion</name>
<prompt lang="en">Display 'version' column</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -seqversion")[ bool(value) ]</code>
</format>
<argpos>13</argpos>
</parameter>
<parameter>
<name>e_type</name>
<prompt lang="en">Display 'type' column</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="python">not e_only</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -type")[ bool(value) ]</code>
</format>
<argpos>14</argpos>
</parameter>
<parameter>
<name>e_length</name>
<prompt lang="en">Display 'length' column</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="python">not e_only</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -length")[ bool(value) ]</code>
</format>
<argpos>15</argpos>
</parameter>
<parameter>
<name>e_pgc</name>
<prompt lang="en">Display 'percent gc content' column</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="python">not e_only</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -pgc")[ bool(value) ]</code>
</format>
<argpos>16</argpos>
</parameter>
<parameter>
<name>e_organism</name>
<prompt lang="en">Display 'organism' column</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="python">not e_only</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -organism")[ bool(value) ]</code>
</format>
<argpos>17</argpos>
</parameter>
<parameter>
<name>e_description</name>
<prompt lang="en">Display 'description' column</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="python">not e_only</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -description")[ bool(value) ]</code>
</format>
<argpos>18</argpos>
</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>19</argpos>
</parameter>
</parameters>
</program>
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