/var/lib/mobyle/programs/diffseq.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>diffseq</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>diffseq</title>
<description>
<text lang="en">Compare and report features of two similar sequences</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/diffseq.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>alignment:differences</category>
<command>diffseq</command>
</head>
<parameters>
<paragraph>
<name>e_input</name>
<prompt lang="en">Input section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_asequence</name>
<prompt lang="en">asequence 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>1,1</card>
</type>
<format>
<code proglang="python">("", " -asequence=" + str(value))[value is not None]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter issimple="1" ismandatory="1">
<name>e_bsequence</name>
<prompt lang="en">bsequence 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>1,1</card>
</type>
<format>
<code proglang="python">("", " -bsequence=" + str(value))[value is not None]</code>
</format>
<argpos>2</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_required</name>
<prompt lang="en">Required section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_wordsize</name>
<prompt lang="en">Word size (value greater than or equal to 2)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10</value>
</vdef>
<format>
<code proglang="python">("", " -wordsize=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 2 is required</text>
</message>
<code proglang="python">value >= 2</code>
</ctrl>
<argpos>3</argpos>
<comment>
<text lang="en">The similar regions between the two sequences are found by creating a hash table of 'wordsize'd subsequences. 10 is a reasonable default. Making this value larger (20?) may speed up the program slightly, but will mean that any two differences within 'wordsize' of each other will be grouped as a single region of difference. This value may be made smaller (4?) to improve the resolution of nearby differences, but the program will go much slower.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_additional</name>
<prompt lang="en">Additional section</prompt>
<parameters>
<parameter>
<name>e_globaldifferences</name>
<prompt lang="en">Force reporting of differences at the start and end</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -globaldifferences")[ bool(value) ]</code>
</format>
<argpos>4</argpos>
<comment>
<text lang="en">Normally this program will find regions of identity that are the length of the specified word-size or greater and will then report the regions of difference between these matching regions. This works well and is what most people want if they are working with long overlapping nucleic acid sequences. You are usually not interested in the non-overlapping ends of these sequences. If you have protein sequences or short RNA sequences however, you will be interested in differences at the very ends . It this option is set to be true then the differences at the ends will also be 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 report file</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>diffseq.report</value>
</vdef>
<format>
<code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
</format>
<argpos>5</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>DIFFSEQ</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>6</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>
<parameter>
<name>e_aoutfeat</name>
<prompt lang="en">Name of the output feature file (e_aoutfeat)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>diffseq.e_aoutfeat</value>
</vdef>
<format>
<code proglang="python">("" , " -aoutfeat=" + str(value))[value is not None]</code>
</format>
<argpos>7</argpos>
<comment>
<text lang="en">File for output of first sequence's features</text>
</comment>
</parameter>
<parameter>
<name>e_offormat_aoutfeat</name>
<prompt lang="en">Choose the feature output format</prompt>
<type>
<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>8</argpos>
</parameter>
<parameter isout="1">
<name>e_aoutfeat_out</name>
<prompt lang="en">aoutfeat_out option</prompt>
<type>
<datatype>
<class>Feature</class>
<superclass>AbstractText</superclass>
</datatype>
<dataFormat>
<ref param="e_offormat_aoutfeat">
</ref>
</dataFormat>
</type>
<filenames>
<code proglang="python">e_aoutfeat</code>
</filenames>
</parameter>
<parameter>
<name>e_boutfeat</name>
<prompt lang="en">Name of the output feature file (e_boutfeat)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>diffseq.e_boutfeat</value>
</vdef>
<format>
<code proglang="python">("" , " -boutfeat=" + str(value))[value is not None]</code>
</format>
<argpos>9</argpos>
<comment>
<text lang="en">File for output of second sequence's features</text>
</comment>
</parameter>
<parameter>
<name>e_offormat_boutfeat</name>
<prompt lang="en">Choose the feature output format</prompt>
<type>
<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>10</argpos>
</parameter>
<parameter isout="1">
<name>e_boutfeat_out</name>
<prompt lang="en">boutfeat_out option</prompt>
<type>
<datatype>
<class>Feature</class>
<superclass>AbstractText</superclass>
</datatype>
<dataFormat>
<ref param="e_offormat_boutfeat">
</ref>
</dataFormat>
</type>
<filenames>
<code proglang="python">e_boutfeat</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>11</argpos>
</parameter>
</parameters>
</program>
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