/var/lib/mobyle/programs/tfscan.xml is in mobyle-programs 5.1.2-2.
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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>tfscan</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>tfscan</title>
<description>
<text lang="en">Identify transcription factor binding sites in DNA sequences</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/tfscan.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>sequence:nucleic:transcription</category>
<command>tfscan</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>DNA</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>
<parameter issimple="1" ismandatory="1">
<name>e_menu</name>
<prompt lang="en">Transcription factor class</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>V</value>
</vdef>
<vlist>
<velem>
<value>F</value>
<label>Fungi</label>
</velem>
<velem>
<value>I</value>
<label>Insect</label>
</velem>
<velem>
<value>P</value>
<label>Plant</label>
</velem>
<velem>
<value>V</value>
<label>Vertebrate</label>
</velem>
<velem>
<value>O</value>
<label>Other</label>
</velem>
<velem>
<value>C</value>
<label>Custom</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -menu=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter>
<name>e_custom</name>
<prompt lang="en">Transfac database data file (optional)</prompt>
<type>
<datatype>
<class>TransfacData</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="python">e_menu=="C"</code>
</precond>
<format>
<code proglang="python">("", " -custom=" + str(value))[value is not None]</code>
</format>
<argpos>3</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_required</name>
<prompt lang="en">Required section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_mismatch</name>
<prompt lang="en">Number of mismatches (value greater than or equal to 0)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -mismatch=" + 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>
<argpos>4</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_additional</name>
<prompt lang="en">Additional section</prompt>
<parameters>
<parameter>
<name>e_minlength</name>
<prompt lang="en">Display matches equal to or above this length (value greater than or equal to 1)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">("", " -minlength=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 1 is required</text>
</message>
<code proglang="python">value >= 1</code>
</ctrl>
<argpos>5</argpos>
</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>tfscan.report</value>
</vdef>
<format>
<code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
</format>
<argpos>6</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>SEQTABLE</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>7</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>
<comment>
<text lang="en">A "quality" value ranging from 1 to 6 and reflecting the experimental reliability of a certain
protein-DNA interaction. These values have the following meaning:</text>
<text lang="en">1 -- functionally confirmed factor binding site</text>
<text lang="en">2 -- binding of pure protein (purified or recombinant)</text>
<text lang="en">3 -- immunologically characterized binding activity of a cellular extract</text>
<text lang="en">4 -- binding activity characterized via a known binding sequence</text>
<text lang="en">5 -- binding of uncharacterized extract protein to a bone fide element</text>
<text lang="en">6 -- no quality assigned.</text>
</comment>
</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>8</argpos>
</parameter>
</parameters>
</program>
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