/var/lib/mobyle/programs/trimest.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>trimest</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>trimest</title>
<description>
<text lang="en">Remove poly-A tails from nucleotide sequences</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/trimest.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>sequence:edit</category>
<command>trimest</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_additional</name>
<prompt lang="en">Additional section</prompt>
<parameters>
<parameter>
<name>e_minlength</name>
<prompt lang="en">Minimum length of a poly-a tail (value greater than or equal to 1)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>4</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>2</argpos>
<comment>
<text lang="en">This is the minimum length that a poly-A (or poly-T) tail must have before it is removed. If there are mismatches in the tail than there must be at least this length of poly-A tail before the mismatch for the mismatch to be considered part of the tail.</text>
</comment>
</parameter>
<parameter>
<name>e_mismatches</name>
<prompt lang="en">Number of contiguous mismatches allowed in a tail (value greater than or equal to 0)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">("", " -mismatches=" + 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>3</argpos>
<comment>
<text lang="en">If there are this number or fewer contiguous non-A bases in a poly-A tail then, if there are '-minlength' 'A' bases before them, they will be considered part of the tail and removed .
For example the terminal 4 A's of GCAGAAAA would be removed with the default values of -minlength=4 and -mismatches=1 (There are not at least 4 A's before the last 'G' and so only the A's after it are considered to be part of the tail). The terminal 9 bases of GCAAAAGAAAA would be removed; There are at least -minlength A's preceeding the last 'G', so it is part of the tail.</text>
</comment>
</parameter>
<parameter>
<name>e_reverse</name>
<prompt lang="en">Write the reverse complement when poly-t is removed</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noreverse", "")[ bool(value) ]</code>
</format>
<argpos>4</argpos>
<comment>
<text lang="en">When a poly-T region at the 5' end of the sequence is found and removed, it is likely that the sequence is in the reverse sense. This option will change the sequence to the forward sense when it is written out. If this option is not set, then the sense will not be changed.</text>
</comment>
</parameter>
<parameter>
<name>e_tolower</name>
<prompt lang="en">Change poly-a tail to lower-case</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -tolower")[ bool(value) ]</code>
</format>
<argpos>5</argpos>
<comment>
<text lang="en">The poly-A region can be 'masked' by converting the sequence characters to lower-case. Some non-EMBOSS programs e.g. fasta can interpret this as a masked region. The sequence is unchanged apart from the case change. You might like to ensure that the whole sequence is in upper-case before masking the specified regions to lower-case by using the '-supper' sequence qualifier.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_advanced</name>
<prompt lang="en">Advanced section</prompt>
<parameters>
<parameter>
<name>e_fiveprime</name>
<prompt lang="en">Remove poly-t tails at the 5' end of the sequence.</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nofiveprime", "")[ bool(value) ]</code>
</format>
<argpos>6</argpos>
<comment>
<text lang="en">If this is set true, then the 5' end of the sequence is inspected for poly-T tails. These will be removed if they are longer than any 3' poly-A tails. If this is false, then the 5' end is ignored.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_output</name>
<prompt lang="en">Output section</prompt>
<parameters>
<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>trimest.e_outseq</value>
</vdef>
<format>
<code proglang="python">("" , " -outseq=" + str(value))[value is not None]</code>
</format>
<argpos>7</argpos>
</parameter>
<parameter>
<name>e_osformat_outseq</name>
<prompt lang="en">Choose the sequence output format</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>FASTA</value>
</vdef>
<vlist>
<velem>
<value>EMBL</value>
<label>Embl</label>
</velem>
<velem>
<value>FASTA</value>
<label>Fasta</label>
</velem>
<velem>
<value>GCG</value>
<label>Gcg</label>
</velem>
<velem>
<value>GENBANK</value>
<label>Genbank</label>
</velem>
<velem>
<value>NBRF</value>
<label>Nbrf</label>
</velem>
<velem>
<value>CODATA</value>
<label>Codata</label>
</velem>
<velem>
<value>RAW</value>
<label>Raw</label>
</velem>
<velem>
<value>SWISSPROT</value>
<label>Swissprot</label>
</velem>
<velem>
<value>GFF</value>
<label>Gff</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -osformat=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>8</argpos>
</parameter>
<parameter isout="1">
<name>e_outseq_out</name>
<prompt lang="en">outseq_out option</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>
<ref param="e_osformat_outseq">
</ref>
</dataFormat>
</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>9</argpos>
</parameter>
</parameters>
</program>
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