/var/lib/mobyle/programs/edialign.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>edialign</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>edialign</title>
<description>
<text lang="en">Local multiple alignment of sequences</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/edialign.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>alignment:multiple</category>
<command>edialign</command>
</head>
<parameters>
<paragraph>
<name>e_input</name>
<prompt lang="en">Input section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_sequences</name>
<prompt lang="en">sequences 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>2,n</card>
</type>
<format>
<code proglang="python">("", " -sequences=" + str(value))[value is not None]</code>
</format>
<argpos>1</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_additional</name>
<prompt lang="en">Additional section</prompt>
<parameters>
<parameter>
<name>e_nucmode</name>
<prompt lang="en">Nucleic acid sequence alignment mode</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>n</value>
</vdef>
<vlist>
<velem>
<value>n</value>
<label>Simple</label>
</velem>
<velem>
<value>nt</value>
<label>Translation</label>
</velem>
<velem>
<value>ma</value>
<label>Mixed alignments</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -nucmode=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">Nucleic acid sequence alignment mode (simple, translated or mixed)</text>
</comment>
</parameter>
<parameter>
<name>e_revcomp</name>
<prompt lang="en">Also consider the reverse complement</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -revcomp")[ bool(value) ]</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter>
<name>e_overlapw</name>
<prompt lang="en">Use overlap weights</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<vlist>
<velem>
<value>1</value>
<label>Default (when nseq =< 35)</label>
</velem>
<velem>
<value>2</value>
<label>Yes</label>
</velem>
<velem>
<value>3</value>
<label>No</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -overlapw=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>4</argpos>
<comment>
<text lang="en">By default overlap weights are used when Nseq =<35 but you can set this to 'yes' or 'no'</text>
</comment>
</parameter>
<parameter>
<name>e_linkage</name>
<prompt lang="en">Clustering method to construct sequence tree</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>UPGMA</value>
</vdef>
<vlist>
<velem>
<value>UPGMA</value>
<label>Upgma</label>
</velem>
<velem>
<value>max</value>
<label>Maximum linkage</label>
</velem>
<velem>
<value>min</value>
<label>Minimum linkage</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -linkage=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>5</argpos>
<comment>
<text lang="en">Clustering method to construct sequence tree (UPGMA, minimum linkage or maximum linkage)</text>
</comment>
</parameter>
<parameter>
<name>e_maxfragl</name>
<prompt lang="en">Maximum fragment length (value greater than or equal to 0)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>40</value>
</vdef>
<format>
<code proglang="python">("", " -maxfragl=" + 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>6</argpos>
</parameter>
<parameter>
<name>e_fragmat</name>
<prompt lang="en">Consider only n-fragment pairs that start with two matches</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -fragmat")[ bool(value) ]</code>
</format>
<argpos>7</argpos>
</parameter>
<parameter>
<name>e_fragsim</name>
<prompt lang="en">Consider only p-fragment pairs if first amino acid or codon pair has similarity score of at least n (value greater than or equal to 0)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>4</value>
</vdef>
<format>
<code proglang="python">("", " -fragsim=" + 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>8</argpos>
</parameter>
<parameter>
<name>e_itscore</name>
<prompt lang="en">Use iterative score</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -itscore")[ bool(value) ]</code>
</format>
<argpos>9</argpos>
</parameter>
<parameter>
<name>e_threshold</name>
<prompt lang="en">Threshold for considering diagonal for alignment (value greater than or equal to 0.0)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.0</value>
</vdef>
<format>
<code proglang="python">("", " -threshold=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 0.0 is required</text>
</message>
<code proglang="python">value >= 0.0</code>
</ctrl>
<argpos>10</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_output</name>
<prompt lang="en">Output section</prompt>
<parameters>
<parameter>
<name>e_mask</name>
<prompt lang="en">Replace unaligned characters by stars '*' rather then putting them in lowercase</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -mask")[ bool(value) ]</code>
</format>
<argpos>11</argpos>
</parameter>
<parameter>
<name>e_dostars</name>
<prompt lang="en">Activate writing of stars instead of numbers</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -dostars")[ bool(value) ]</code>
</format>
<argpos>12</argpos>
</parameter>
<parameter>
<name>e_starnum</name>
<prompt lang="en">Put up to n stars '*' instead of digits 0-9 to indicate level of conservation (value greater than or equal to 0)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>4</value>
</vdef>
<format>
<code proglang="python">("", " -starnum=" + 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>13</argpos>
</parameter>
<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>edialign.e_outfile</value>
</vdef>
<format>
<code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
</format>
<argpos>14</argpos>
</parameter>
<parameter isout="1">
<name>e_outfile_out</name>
<prompt lang="en">outfile_out option</prompt>
<type>
<datatype>
<class>EdialignReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="python">e_outfile</code>
</filenames>
</parameter>
<parameter>
<name>e_outseq</name>
<prompt lang="en">Name of the output sequence file (e_outseq)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>edialign.e_outseq</value>
</vdef>
<format>
<code proglang="python">("" , " -outseq=" + str(value))[value is not None]</code>
</format>
<argpos>15</argpos>
</parameter>
<parameter isout="1">
<name>e_outseq_out</name>
<prompt lang="en">outseq_out option</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<filenames>
<code proglang="python">e_outseq</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>16</argpos>
</parameter>
</parameters>
</program>
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