/var/lib/mobyle/programs/hmmalign.xml is in mobyle-programs 5.1.2-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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<!-- XML Authors: Corinne Maufrais, Nicolas Joly and Bertrand Neron, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>hmmalign</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/hmmer_package.xml"/>
<doc>
<title>HMMALIGN</title>
<description>
<text lang="en">Align sequences to a profile HMM</text>
</description>
</doc>
<category>hmm:alignment:multiple</category>
<category>alignment:multiple:hmm</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>hmmcmd</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"hmmalign"</code>
<code proglang="python">"hmmalign"</code>
</format>
<argpos>0</argpos>
</parameter>
<paragraph>
<name>infile</name>
<prompt lang="en">Input file</prompt>
<parameters>
<paragraph>
<name>file</name>
<prompt lang="en">Input sequences file</prompt>
<argpos>3</argpos>
<comment>
<text lang="en">Input sequence file may be in any unaligned or aligned file format. If it is
in a multiple alignment format (e.g. Stockholm, MSF, ClustalW), the existing alignment is
ignored (i.e., the
sequences are read as if they were unaligned).</text>
</comment>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>seqfile</name>
<prompt lang="en">Sequences File</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
<dataFormat>EMBL</dataFormat>
<dataFormat>Genbank</dataFormat>
<dataFormat>Uniprot</dataFormat>
<card>2,n</card>
</type>
<format>
<code proglang="perl">" $seqfile" </code>
<code proglang="python">" " + str(seqfile) </code>
</format>
</parameter>
</parameters>
</paragraph>
<parameter ismandatory="1" issimple="1">
<name>hmmfile</name>
<prompt lang="en">Profile HMM file</prompt>
<type>
<datatype>
<class>HmmProfile</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" "+str(value)</code>
</format>
<argpos>2</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>expert_options</name>
<prompt lang="en">Expert Options</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>biotype</name>
<prompt lang="en">Assert sequences and hmm files are both in same type</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>No Autodetection</label>
</velem>
<velem>
<value>--amino</value>
<label>Protein</label>
</velem>
<velem>
<value>--dna</value>
<label>DNA</label>
</velem>
<velem>
<value>--rna</value>
<label>RNA</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " $value" : ""</code>
<code proglang="python">("", " " + str(value))[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">The alphabet type (amino, DNA, or RNA) is autodetected by default, by looking at the composition of the
msafile. Autodetection is normally quite reliable, but occasionally alphabet type may be ambiguous and
autodetection can fail (for instance, on tiny toy alignments of just a few residues). To avoid this, or to
increase robustness in automated analysis pipelines, you may specify the alphabet type of msafile with
these options.</text>
<text lang="en">Protein: Specify that all sequences in seqfile are proteins. By default, alphabet type is
autodetected from looking at the residue composition.</text>
<text lang="en">DNA: Specify that all sequences in seqfile are DNAs.</text>
<text lang="en">RNA: Specify that all sequences in seqfile are RNAs.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>common_options</name>
<prompt lang="en">Common Options</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>allcol</name>
<prompt lang="en">Include all consensus columns in ali, even if all gaps</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " --allcol : ""</code>
<code proglang="python">( "" , " --allcol " )[ value ]</code>
</format>
<comment>
<text lang="en">Include columns in the output alignment for every match (consensus) state in
the hmmfile, even if it means having all-gap columns. This is useful in analysis
pipelines that need to be able to maintain a predetermined profile HMM architecture
(with an unchanging number of consensus columns) through an hmmalign
step.</text>
</comment>
</parameter>
<parameter>
<name>mapali</name>
<prompt lang="en">Include alignment file</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>STOCKHOLM</dataFormat>
</type>
<format>
<code proglang="perl">(defined $value) ? " --mapali $value" : ""</code>
<code proglang="python">( "" , " --mapali " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Merge the existing alignment in file into the result, where the file is exactly the
same alignment that was used to build the model in hmmfile. This is done using
a 'map' of alignment columns to consensus profile positions that is stored in the
hmmfile. The multiple alignment in the file will be exactly reproduced in its consensus
columns (as defined by the profile), but the displayed alignment in insert columns
may be altered, because insertions relative to a profile are considered by convention
to be unaligned data.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output_options</name>
<prompt lang="en">Output Options</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>trim</name>
<prompt lang="en">Trim terminal tails of nonaligned residues from alignment</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " --trim" : ""</code>
<code proglang="python">( "", " --trim" )[ value ]</code>
</format>
<comment>
<text lang="en">Trim nonhomologous residues (assigned to N and C states in the optimal alignments)
from the resulting multiple alignment output.</text>
</comment>
</parameter>
<parameter>
<name>outfile_name</name>
<prompt lang="en">Outfile name (-o)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -o $value" : ""</code>
<code proglang="python">("", " -o " + str(value))[value is not None]</code>
</format>
</parameter>
<parameter isout="1">
<name>outputfile</name>
<prompt lang="en">Alignment file</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>
<ref param="outputformat"/>
</dataFormat>
</type>
<precond>
<code proglang="perl">defined($outfile_name)</code>
<code proglang="python">outfile_name is not None</code>
</precond>
<filenames>
<code proglang="perl">"$outfile_name"</code>
<code proglang="python">str(outfile_name)</code>
</filenames>
</parameter>
<parameter isstdout="1">
<name>outfile</name>
<prompt lang="en">Alignment file</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>
<ref param="outputformat"/>
</dataFormat>
</type>
<precond>
<code proglang="perl">not defined($outfile_name)</code>
<code proglang="python">outfile_name is None</code>
</precond>
<filenames>
<code proglang="perl">"hmmalign.out"</code>
<code proglang="python">"hmmalign.out"</code>
</filenames>
</parameter>
<parameter issimple="1">
<name>outputformat</name>
<prompt lang="en">Output format</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>STOCKHOLM</value>
</vdef>
<vlist>
<velem>
<value>STOCKHOLM</value>
<label>STOCKHOLM</label>
</velem>
<velem>
<value>Pfam</value>
<label>Pfam</label>
</velem>
<velem>
<value>A2M</value>
<label>A2M</label>
</velem>
<velem>
<value>PSIBLAST</value>
<label>PSIBLAST</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " --outformat $value" : ""</code>
<code proglang="python">( "" , " --outformat " + str( value) )[ value is not None and value != vdef ]</code>
</format>
<comment>
<text lang="en">Specify that the msafile is in the selected format. Currently the accepted multiple
alignment sequence file formats only include Stockholm and SELEX. Default is to autodetect
the format of the file.</text>
</comment>
</parameter>
</parameters>
</paragraph>
</parameters>
</program>
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