/var/lib/mobyle/programs/pima.xml is in mobyle-programs 5.1.2-2.
This file is owned by root:root, with mode 0o644.
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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>pima</name>
<version>1.40</version>
<doc>
<title>PIMA</title>
<description>
<text lang="en">Pattern-Induced Multi-sequence Alignment program</text>
</description>
<authors>R. D. Smith and T. F. Smith</authors>
<reference>R. D. Smith and T. F. Smith. Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative modelling. protein Engineering, vol5, number 1, pp 35-41, 1992</reference>
<sourcelink>ftp://ftp.ebi.ac.uk/pub/software/unix/pima/</sourcelink>
</doc>
<category>alignment:multiple</category>
<command>pima</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>sequence</name>
<prompt lang="en">Sequences file</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>IG</dataFormat>
<dataFormat>GENBANK</dataFormat>
<dataFormat>NBRF</dataFormat>
<dataFormat>EMBL</dataFormat>
<dataFormat>CODATA</dataFormat>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">" $value" </code>
<code proglang="python">" " + str(value) </code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en"> Name of the input file containing the sequences to be clustered and multi-aligned. Sequences can be in any of the following formats: IG/Stanford, GenBank/GB, NBRF, EMBL, Pearson/Fasta, PIR/CODATA. The format of the output sequence files will match the format of this input file. </text>
</comment>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>cluster_name</name>
<prompt lang="en">Cluster name</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">" $value" </code>
<code proglang="python">" " + str(value)</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">An arbitrary name used to label the cluster.</text>
</comment>
</parameter>
<paragraph>
<name>pima_params</name>
<prompt lang="en">Parameters</prompt>
<parameters>
<parameter>
<name>ref_seq_name</name>
<prompt lang="en">Reference sequence name</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $sec_struc_seq_filename</code>
<code proglang="python">sec_struc_seq_filename is not None</code>
</precond>
<format>
<code proglang="perl">(defined $value)? " $value" : "" </code>
<code proglang="python">("", " "+str(value))[value is not None]</code>
</format>
<argpos>4</argpos>
<comment>
<text lang="en">[optional; if specified, then sec_struct_seq_filename must also be specified]. Locus name of one of the primary sequences for which the secondary structure is in the file seq_struct_seq_filename.</text>
</comment>
</parameter>
<parameter>
<name>sec_struc_seq_filename</name>
<prompt lang="en">sec_struc_seq_filename</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $ref_seq_name_</code>
<code proglang="python">ref_seq_name is not None</code>
</precond>
<format>
<code proglang="perl">(defined $value)? " $value" : "" </code>
<code proglang="python">( "" , " " + str(value) )[ value is not None ]</code>
</format>
<argpos>5</argpos>
<comment>
<text lang="en">[optional; if specified, then ref_seq_name must also be specified] Name of a file containing secondary structure sequences for one or more of the primary sequences in the set. The secondary structure sequences in this file must be in one of the formats listed above (see sequence_filename, above). The locus name of each sequence must be the locus name of it's corresponding primary sequence with the suffix '.ss' (e.g. 1ldm.ss). An alpha-helix, 3-10 helix and beta-strand must be designated 'h', 'g', and 'e', respectively. All other characters in the secondary structure sequences will be ignored with respect to the the structure-dependent gap penalty. To allow gaps to be placed between the first and the second and the last elements of these structures, the first and last 2 elements of each should be changed to another character designation. In the secondary structure sequence file pdb-dssp.ss provided with this package, these end cap elements are designated 'i', 'f', and 'd', for alpha-helices, 3-10 helices and beta-strands, respectfully.
</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>pima_options</name>
<prompt lang="en">Options</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>score_cutoff</name>
<prompt lang="en">Cluster score cutoff (-c) </prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -c $value " : "" </code>
<code proglang="python">( "" , " -c " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en"> Use a cluster score cutoff of number. This is the lowest match score to be used to incorporate a sequence into a cluster. The default value of 0.0 will force all input sequences into 1 cluster, but the final pattern may be completely degenerate.</text>
</comment>
</parameter>
<parameter>
<name>ext_gap_cost</name>
<prompt lang="en">Gap extension penalty (-d) </prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -d $value" : "" </code>
<code proglang="python">( "" , " -d " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Use a length dependent gap penalty of number. This is the cost of extending a gap. The default value is dependent on the matrix file used.</text>
</comment>
</parameter>
<parameter>
<name>gap_open_cost</name>
<prompt lang="en">Gap opening penalty (-i) </prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -i $value" : "" </code>
<code proglang="python">( "" , " -i " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Use a length independent gap penalty of number. This is the cost of opening a gap. The default value is dependent on the matrix file used.</text>
</comment>
</parameter>
<parameter>
<name>min_score</name>
<prompt lang="en">Minimum local score (-l) </prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -l $value" : "" </code>
<code proglang="python">( "" , " -l " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en"> Use minimum local score of number. This is the lowest score a quadrant can have before an attempt is made to join this local alignment with the local alignment at the previous step. The default value is dependent on the matrix file used.</text>
</comment>
</parameter>
<parameter>
<name>mat_file</name>
<prompt lang="en">Matrix file (-m) </prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>patgen.mat</value>
</vdef>
<vlist>
<velem>
<value>patgen.mat</value>
<label>patgen.mat</label>
</velem>
<velem>
<value>class1.mat</value>
<label>class1.mat</label>
</velem>
<velem>
<value>class2.mat</value>
<label>class2.mat</label>
</velem>
<velem>
<value>user</value>
<label>User matrix</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef and $value ne "user")? " -m $value" : "" </code>
<code proglang="python">( "" , " -m " + str(value) )[ value is not None and value !=vdef and value !="user"]</code>
</format>
<comment>
<text lang="en">Use matrix file with the name file. The default matrix file is patgen.mat and is provided with this package. The matrix file class1.mat uses the original pima alphabet. The matrix file class2.mat is also provided, which is similar to the matrix file class1.mat but uses the new alphabet.</text>
</comment>
</parameter>
<parameter>
<name>user_mat_file</name>
<prompt lang="en">User matrix file (-m) </prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="perl">$mat_file eq "user"</code>
<code proglang="python">mat_file == "user"</code>
</precond>
<format>
<code proglang="perl">(defined $value)? " -m $value" : "" </code>
<code proglang="python">( "" , " -m " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">User matrix file.</text>
</comment>
</parameter>
<parameter>
<name>not_num_ext</name>
<prompt lang="en">Do not use numerical extensions on each step of the alignment. (-n)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -n" : "" </code>
<code proglang="python">( "" , " -n" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>sec_struc_gap_cost</name>
<prompt lang="en">Secondary structure gap penalty (-t)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -t $value " : "" </code>
<code proglang="python">( "" , " -t " + str(value) + " " )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Use a secondary structure gap penalty of number. This is the cost of a gap at a position matching a secondary structure character. The default value is dependent on the matrix file used and is always 10 times the value of the length independent gap penalty of the matrix file.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>results</name>
<prompt lang="en">Output files</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"*.cluster"</code>
<code proglang="perl">*.pattern"</code>
<code proglang="perl">*.pima"</code>
<code proglang="python">"*.cluster"</code>
<code proglang="python">"*.pattern"</code>
<code proglang="python">"*.pima"</code>
</filenames>
</parameter>
</parameters>
</program>
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