/var/lib/mobyle/programs/dan.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>dan</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>dan</title>
<description>
<text lang="en">Calculates nucleic acid melting temperature</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/dan.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>sequence:nucleic:composition</category>
<command>dan</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_windowsize</name>
<prompt lang="en">Enter window size (value from 1 to 100)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>20</value>
</vdef>
<format>
<code proglang="python">("", " -windowsize=" + 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>
<ctrl>
<message>
<text lang="en">Value less than or equal to 100 is required</text>
</message>
<code proglang="python">value <= 100</code>
</ctrl>
<argpos>2</argpos>
<comment>
<text lang="en">The values of melting point and other thermodynamic properties of the sequence are determined by taking a short length of sequence known as a window and determining the properties of the sequence in that window. The window is incrementally moved along the sequence with the properties being calculated at each new position.</text>
</comment>
</parameter>
<parameter issimple="1" ismandatory="1">
<name>e_shiftincrement</name>
<prompt lang="en">Enter shift increment (value greater than or equal to 1)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">("", " -shiftincrement=" + 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 is the amount by which the window is moved at each increment in order to find the melting point and other properties along the sequence.</text>
</comment>
</parameter>
<parameter issimple="1" ismandatory="1">
<name>e_dnaconc</name>
<prompt lang="en">Enter dna concentration (nm) (value from 1. to 100000.)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>50.</value>
</vdef>
<format>
<code proglang="python">("", " -dnaconc=" + 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>
<ctrl>
<message>
<text lang="en">Value less than or equal to 100000. is required</text>
</message>
<code proglang="python">value <= 100000.</code>
</ctrl>
<argpos>4</argpos>
</parameter>
<parameter issimple="1" ismandatory="1">
<name>e_saltconc</name>
<prompt lang="en">Enter salt concentration (mm) (value from 1. to 1000.)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>50.</value>
</vdef>
<format>
<code proglang="python">("", " -saltconc=" + 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>
<ctrl>
<message>
<text lang="en">Value less than or equal to 1000. is required</text>
</message>
<code proglang="python">value <= 1000.</code>
</ctrl>
<argpos>5</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_additional</name>
<prompt lang="en">Additional section</prompt>
<parameters>
<paragraph>
<name>e_productsection</name>
<prompt lang="en">Product options</prompt>
<parameters>
<parameter>
<name>e_product</name>
<prompt lang="en">Prompt for product values</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -product")[ bool(value) ]</code>
</format>
<argpos>6</argpos>
<comment>
<text lang="en">This prompts for percent formamide, percent of mismatches allowed and product length.</text>
</comment>
</parameter>
<parameter>
<name>e_formamide</name>
<prompt lang="en">Enter percentage of formamide (value from 0. to 100.)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="python">e_product</code>
</precond>
<vdef>
<value>0.</value>
</vdef>
<format>
<code proglang="python">("", " -formamide=" + 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>7</argpos>
<comment>
<text lang="en">This specifies the percent formamide to be used in calculations (it is ignored unless -product is used).</text>
</comment>
</parameter>
<parameter>
<name>e_mismatch</name>
<prompt lang="en">Enter percent mismatch (value from 0. to 100.)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="python">e_product</code>
</precond>
<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>
<ctrl>
<message>
<text lang="en">Value less than or equal to 100. is required</text>
</message>
<code proglang="python">value <= 100.</code>
</ctrl>
<argpos>8</argpos>
<comment>
<text lang="en">This specifies the percent mismatch to be used in calculations (it is ignored unless -product is used).</text>
</comment>
</parameter>
<parameter>
<name>e_prodlen</name>
<prompt lang="en">Enter the product length</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="python">e_product and e_windowsize</code>
</precond>
<format>
<code proglang="python">("", " -prodlen=" + str(value))[value is not None]</code>
</format>
<argpos>9</argpos>
<comment>
<text lang="en">This specifies the product length to be used in calculations (it is ignored unless -product is used).</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_thermosection</name>
<prompt lang="en">Thermodynamic options</prompt>
<parameters>
<parameter>
<name>e_thermo</name>
<prompt lang="en">Thermodynamic calculations</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -thermo")[ bool(value) ]</code>
</format>
<argpos>10</argpos>
<comment>
<text lang="en">Output the DeltaG, DeltaH and DeltaS values of the sequence windows to the output data file.</text>
</comment>
</parameter>
<parameter>
<name>e_temperature</name>
<prompt lang="en">Enter temperature (value from 0. to 100.)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="python">e_thermo</code>
</precond>
<vdef>
<value>25.</value>
</vdef>
<format>
<code proglang="python">("", " -temperature=" + 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>11</argpos>
<comment>
<text lang="en">If -thermo has been specified then this specifies the temperature at which to calculate the DeltaG, DeltaH and DeltaS values.</text>
</comment>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
<paragraph>
<name>e_advanced</name>
<prompt lang="en">Advanced section</prompt>
<parameters>
<parameter>
<name>e_rna</name>
<prompt lang="en">Use rna data values</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -rna")[ bool(value) ]</code>
</format>
<argpos>12</argpos>
<comment>
<text lang="en">This specifies that the sequence is an RNA sequence and not a DNA sequence.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_output</name>
<prompt lang="en">Output section</prompt>
<parameters>
<parameter>
<name>e_plot</name>
<prompt lang="en">Produce a plot</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -plot")[ bool(value) ]</code>
</format>
<argpos>13</argpos>
<comment>
<text lang="en">If this is not specified then the file of output data is produced, else a plot of the melting point along the sequence is produced.</text>
</comment>
</parameter>
<parameter>
<name>e_mintemp</name>
<prompt lang="en">Enter minimum temperature (value from 0. to 150.)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="python">e_plot</code>
</precond>
<vdef>
<value>55.</value>
</vdef>
<format>
<code proglang="python">("", " -mintemp=" + 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 150. is required</text>
</message>
<code proglang="python">value <= 150.</code>
</ctrl>
<argpos>14</argpos>
<comment>
<text lang="en">Enter a minimum value for the temperature scale (y-axis) of the plot.</text>
</comment>
</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>15</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>dan_xygraph</value>
</vdef>
<format>
<code proglang="python">("" , " -goutfile=" + str(value))[value is not None]</code>
</format>
<argpos>16</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_outfile</name>
<prompt lang="en">Name of the report file</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<precond>
<code proglang="python">not e_plot</code>
</precond>
<vdef>
<value>dan.report</value>
</vdef>
<format>
<code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
</format>
<argpos>17</argpos>
<comment>
<text lang="en">If a plot is not being produced then data on the melting point etc. in each window along the sequence is output to the file.</text>
</comment>
</parameter>
<parameter>
<name>e_rformat_outfile</name>
<prompt lang="en">Choose the report output format</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="python">not e_plot</code>
</precond>
<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>18</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>19</argpos>
</parameter>
</parameters>
</program>
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