/var/lib/mobyle/programs/garnier.xml is in mobyle-programs 5.1.2-1.
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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>garnier</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>garnier</title>
<description>
<text lang="en">Predicts protein secondary structure using GOR method</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/garnier.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>sequence:protein:2D_structure</category>
<category>structure:2D_structure</category>
<command>garnier</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>
<biotype>Protein</biotype>
<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_idc</name>
<prompt lang="en">Index decision constants parameter (value from 0 to 6)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -idc=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 0 is required</text>
</message>
<code proglang="python">value >= 0</code>
</ctrl>
<ctrl>
<message>
<text lang="en">Value less than or equal to 6 is required</text>
</message>
<code proglang="python">value <= 6</code>
</ctrl>
<argpos>2</argpos>
<comment>
<text lang="en">In their paper, GOR mention that if you know something about the secondary structure content of the protein you are analyzing, you can do better in prediction. 'idc' is an index into a set of arrays, dharr[] and dsarr[], which provide 'decision constants' (dch, dcs), which are offsets that are applied to the weights for the helix and sheet (extend) terms. So, idc=0 says don't use the decision constant offsets, and idc=1 to 6 indicates that various combinations of dch,dcs offsets should be used.</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 report file</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>garnier.report</value>
</vdef>
<format>
<code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter>
<name>e_rformat_outfile</name>
<prompt lang="en">Choose the report output format</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>TAGSEQ</value>
</vdef>
<vlist>
<velem>
<value>DASGFF</value>
<label>Dasgff</label>
</velem>
<velem>
<value>DBMOTIF</value>
<label>Dbmotif</label>
</velem>
<velem>
<value>DIFFSEQ</value>
<label>Diffseq</label>
</velem>
<velem>
<value>EMBL</value>
<label>Embl</label>
</velem>
<velem>
<value>EXCEL</value>
<label>Excel</label>
</velem>
<velem>
<value>FEATTABLE</value>
<label>Feattable</label>
</velem>
<velem>
<value>GENBANK</value>
<label>Genbank</label>
</velem>
<velem>
<value>GFF</value>
<label>Gff</label>
</velem>
<velem>
<value>LISTFILE</value>
<label>Listfile</label>
</velem>
<velem>
<value>MOTIF</value>
<label>Motif</label>
</velem>
<velem>
<value>NAMETABLE</value>
<label>Nametable</label>
</velem>
<velem>
<value>CODATA</value>
<label>Codata</label>
</velem>
<velem>
<value>REGIONS</value>
<label>Regions</label>
</velem>
<velem>
<value>SEQTABLE</value>
<label>Seqtable</label>
</velem>
<velem>
<value>SIMPLE</value>
<label>Simple</label>
</velem>
<velem>
<value>SRS</value>
<label>Srs</label>
</velem>
<velem>
<value>SWISS</value>
<label>Swiss</label>
</velem>
<velem>
<value>TABLE</value>
<label>Table</label>
</velem>
<velem>
<value>TAGSEQ</value>
<label>Tagseq</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -rformat=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>4</argpos>
</parameter>
<parameter isout="1">
<name>e_outfile_out</name>
<prompt lang="en">outfile_out option</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
<dataFormat>
<ref param="e_rformat_outfile">
</ref>
</dataFormat>
</type>
<precond>
<code proglang="python">e_rformat_outfile in ['DASGFF', 'DBMOTIF', 'DIFFSEQ', 'EMBL', 'EXCEL', 'FEATTABLE', 'GENBANK', 'GFF', 'LISTFILE', 'MOTIF', 'NAMETABLE', 'CODATA', 'REGIONS', 'SEQTABLE', 'SIMPLE', 'SRS', 'SWISS', 'TABLE', 'TAGSEQ']</code>
</precond>
<filenames>
<code proglang="python">e_outfile</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>5</argpos>
</parameter>
</parameters>
</program>
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