/var/lib/mobyle/programs/cpgplot.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>cpgplot</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>cpgplot</title>
<description>
<text lang="en">Identify and plot CpG islands in nucleotide sequence(s)</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/cpgplot.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>sequence:nucleic:cpg_islands</category>
<command>cpgplot</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>
</parameters>
</paragraph>
<paragraph>
<name>e_required</name>
<prompt lang="en">Required section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_window</name>
<prompt lang="en">Window size (value greater than or equal to 1)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>100</value>
</vdef>
<format>
<code proglang="python">("", " -window=" + 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>2</argpos>
<comment>
<text lang="en">The percentage CG content and the Observed frequency of CG is calculated within a window whose size is set by this parameter. The window is moved down the sequence and these statistics are calculated at each position that the window is moved to.</text>
</comment>
</parameter>
<parameter issimple="1" ismandatory="1">
<name>e_minlen</name>
<prompt lang="en">Minimum length of an island (value greater than or equal to 1)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>200</value>
</vdef>
<format>
<code proglang="python">("", " -minlen=" + 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>3</argpos>
<comment>
<text lang="en">This sets the minimum length that a CpG island has to be before it is reported.</text>
</comment>
</parameter>
<parameter issimple="1" ismandatory="1">
<name>e_minoe</name>
<prompt lang="en">Minimum observed/expected (value from 0. to 10.)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.6</value>
</vdef>
<format>
<code proglang="python">("", " -minoe=" + 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 10. is required</text>
</message>
<code proglang="python">value <= 10.</code>
</ctrl>
<argpos>4</argpos>
<comment>
<text lang="en">This sets the minimum average observed to expected ratio of C plus G to CpG in a set of 10 windows that are required before a CpG island is reported.</text>
</comment>
</parameter>
<parameter issimple="1" ismandatory="1">
<name>e_minpc</name>
<prompt lang="en">Minimum percentage (value from 0. to 100.)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>50.</value>
</vdef>
<format>
<code proglang="python">("", " -minpc=" + 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 100. is required</text>
</message>
<code proglang="python">value <= 100.</code>
</ctrl>
<argpos>5</argpos>
<comment>
<text lang="en">This sets the minimum average percentage of G plus C a set of 10 windows that are required before a CpG island is reported.</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>cpgplot.e_outfile</value>
</vdef>
<format>
<code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
</format>
<argpos>6</argpos>
<comment>
<text lang="en">This sets the name of the file holding the report of the input sequence name, CpG island parameters and the output details of any CpG islands that are found.</text>
</comment>
</parameter>
<parameter isout="1">
<name>e_outfile_out</name>
<prompt lang="en">outfile_out option</prompt>
<type>
<datatype>
<class>CpgplotReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="python">e_outfile</code>
</filenames>
</parameter>
<parameter>
<name>e_plot</name>
<prompt lang="en">Plot cpg island score</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noplot", "")[ bool(value) ]</code>
</format>
<argpos>7</argpos>
</parameter>
<parameter>
<name>e_graph</name>
<prompt lang="en">Choose the e_graph output format</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="python">e_plot</code>
</precond>
<vdef>
<value>png</value>
</vdef>
<vlist>
<velem>
<value>png</value>
<label>Png</label>
</velem>
<velem>
<value>gif</value>
<label>Gif</label>
</velem>
<velem>
<value>cps</value>
<label>Cps</label>
</velem>
<velem>
<value>ps</value>
<label>Ps</label>
</velem>
<velem>
<value>meta</value>
<label>Meta</label>
</velem>
<velem>
<value>data</value>
<label>Data</label>
</velem>
</vlist>
<format>
<code proglang="python">(" -graph=" + str(vdef), " -graph=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>8</argpos>
</parameter>
<parameter>
<name>xy_goutfile</name>
<prompt lang="en">Name of the output graph</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<precond>
<code proglang="python">e_plot</code>
</precond>
<vdef>
<value>cpgplot_xygraph</value>
</vdef>
<format>
<code proglang="python">("" , " -goutfile=" + str(value))[value is not None]</code>
</format>
<argpos>9</argpos>
</parameter>
<parameter isout="1">
<name>xy_outgraph_png</name>
<prompt lang="en">Graph file</prompt>
<type>
<datatype>
<class>Picture</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="python">e_plot and e_graph == "png"</code>
</precond>
<filenames>
<code proglang="python">"*.png"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>xy_outgraph_gif</name>
<prompt lang="en">Graph file</prompt>
<type>
<datatype>
<class>Picture</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="python">e_plot and e_graph == "gif"</code>
</precond>
<filenames>
<code proglang="python">"*.gif"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>xy_outgraph_ps</name>
<prompt lang="en">Graph file</prompt>
<type>
<datatype>
<class>PostScript</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="python">e_plot and e_graph == "ps" or e_graph == "cps"</code>
</precond>
<filenames>
<code proglang="python">"*.ps"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>xy_outgraph_meta</name>
<prompt lang="en">Graph file</prompt>
<type>
<datatype>
<class>Picture</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="python">e_plot and e_graph == "meta"</code>
</precond>
<filenames>
<code proglang="python">"*.meta"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>xy_outgraph_data</name>
<prompt lang="en">Graph file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="python">e_plot and e_graph == "data"</code>
</precond>
<filenames>
<code proglang="python">"*.dat"</code>
</filenames>
</parameter>
<parameter>
<name>e_obsexp</name>
<prompt lang="en">Show observed/expected threshold line</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noobsexp", "")[ bool(value) ]</code>
</format>
<argpos>10</argpos>
<comment>
<text lang="en">If this is set to true then the graph of the observed to expected ratio of C plus G to CpG within a window is displayed.</text>
</comment>
</parameter>
<parameter>
<name>e_cg</name>
<prompt lang="en">Show cpg rich regions</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nocg", "")[ bool(value) ]</code>
</format>
<argpos>11</argpos>
<comment>
<text lang="en">If this is set to true then the graph of the regions which have been determined to be CpG islands is displayed.</text>
</comment>
</parameter>
<parameter>
<name>e_pc</name>
<prompt lang="en">Show percentage line</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nopc", "")[ bool(value) ]</code>
</format>
<argpos>12</argpos>
<comment>
<text lang="en">If this is set to true then the graph of the percentage C plus G within a window is displayed.</text>
</comment>
</parameter>
<parameter>
<name>e_outfeat</name>
<prompt lang="en">Name of the output feature file (e_outfeat)</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>cpgplot.e_outfeat</value>
</vdef>
<format>
<code proglang="python">("" , " -outfeat=" + str(value))[value is not None]</code>
</format>
<argpos>13</argpos>
<comment>
<text lang="en">File for output features</text>
</comment>
</parameter>
<parameter>
<name>e_offormat_outfeat</name>
<prompt lang="en">Choose the feature output format</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>GFF</value>
</vdef>
<vlist>
<velem>
<value>GFF</value>
<label>Gff</label>
</velem>
<velem>
<value>EMBL</value>
<label>Embl</label>
</velem>
<velem>
<value>SWISSPROT</value>
<label>Swissprot</label>
</velem>
<velem>
<value>NBRF</value>
<label>Nbrf</label>
</velem>
<velem>
<value>CODATA</value>
<label>Codata</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -offormat=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>14</argpos>
</parameter>
<parameter isout="1">
<name>e_outfeat_out</name>
<prompt lang="en">outfeat_out option</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Feature</class>
<superclass>AbstractText</superclass>
</datatype>
<dataFormat>
<ref param="e_offormat_outfeat">
</ref>
</dataFormat>
</type>
<filenames>
<code proglang="python">e_outfeat</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>15</argpos>
</parameter>
</parameters>
</program>
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