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<!DOCTYPE program PUBLIC "program" "../mobyle.dtd">
<program>
<head>
<name>pftools</name>
<version>2.3</version>
<doc>
<title>PFTOOLS</title>
<description>
<text lang="en">Profile Tools</text>
</description>
<authors>P. Bucher</authors>
<reference>Bucher P, Karplus K, Moeri N and Hofmann, K. (1996). A flexible motif search technique based on generalized profiles. Comput. Chem. 20:3-24.</reference>
<sourcelink>http://www.isrec.isb-sib.ch/ftp-server/pftools/</sourcelink>
</doc>
<category>sequence:nucleic:pattern</category>
<category>sequence:protein:pattern</category>
</head>
<parameters xmlns:xi="http://www.w3.org/2001/XInclude">
<parameter ismandatory="1" iscommand="1" issimple="1">
<name>pftools</name>
<prompt lang="en">PFTOOLS program</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>pfscan</value>
</vdef>
<vlist>
<velem>
<value>pfscan</value>
<label>pfscan: scan a sequence with a profile db</label>
</velem>
<velem>
<value>pfsearch</value>
<label>pfsearch: search a sequence db for segments matching a profile</label>
</velem>
</vlist>
<format>
<code proglang="perl">"$value -v"</code>
<code proglang="python">str(value) + " -v"</code>
</format>
<comment>
<text lang="en">pfscan compares a protein or nucleic acid sequence against a profile library (default: Prosite).</text>
<text lang="en">pfsearch compares a query profile against a DNA or protein sequence library.</text>
<text lang="en">The result is an unsorted list of profile-sequence matches written to the standard output.</text>
</comment>
</parameter>
<parameter ishidden="1">
<name>fasta_format</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">" -f"</code>
<code proglang="python">" -f"</code>
</format>
<argpos>1</argpos>
</parameter>
<paragraph>
<name>pfscan</name>
<prompt lang="en">PFSCAN parameters</prompt>
<precond>
<code proglang="perl">$pftools eq "pfscan"</code>
<code proglang="python">pftools == "pfscan"</code>
</precond>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>seqfile</name>
<prompt lang="en">Sequence File</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" " + str(value)</code>
</format>
<argpos>90</argpos>
<comment>
<text lang="en">This DNA or protein sequence will be used to search for matches to a library of PROSITE profiles.</text>
</comment>
</parameter>
<parameter issimple="1">
<name>prosite</name>
<prompt lang="en">Scan PROSITE db?</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " <xi:include href="../../Local/Services/Programs/Env/pftools_data.xml" xpointer="xpointer(/db/prosite/text())" />" : ""</code>
<code proglang="python">( "" , " <xi:include href="../../Local/Services/Programs/Env/pftools_data.xml" xpointer="xpointer(/db/prosite/text())" />" )[ value ]</code>
</format>
<argpos>100</argpos>
<comment>
<text lang="en">Prosite library</text>
</comment>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>profiledb</name>
<prompt lang="en">Profile(s) file in PROSITE format</prompt>
<type>
<datatype>
<class>PrositeProfile</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">not $prosite</code>
<code proglang="python">not prosite</code>
</precond>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" " + str(value)</code>
</format>
<argpos>100</argpos>
<comment>
<text lang="en">This file should contain one or several PROSITE profiles, against which the query sequence will be matched. Each entry in this library should be separated from the next by a line containing only the code.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>pfsearch</name>
<prompt lang="en">PFSEARCH parameters</prompt>
<precond>
<code proglang="perl">$pftools eq "pfsearch"</code>
<code proglang="python">pftools == "pfsearch"</code>
</precond>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>profile</name>
<prompt lang="en">Profile(s) file in PROSITE format</prompt>
<type>
<datatype>
<class>PrositeProfile</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">" $value" </code>
<code proglang="python">" " + str(value)</code>
</format>
<argpos>90</argpos>
<comment>
<text lang="en">The PROSITE profile contained in this file will be used to search for profile to sequence matches in a biological sequence library.</text>
</comment>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>aa_or_nuc_db</name>
<prompt lang="en">Library of DNA or protein sequences?</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>Null</value>
</vdef>
<vlist>
<velem undef="1">
<value>Null</value>
<label>Choose type of library</label>
</velem>
<velem>
<value>user</value>
<label>User library</label>
</velem>
<velem>
<value>protein</value>
<label>Protein</label>
</velem>
<velem>
<value>dna</value>
<label>DNA</label>
</velem>
</vlist>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<ctrl>
<message>
<text lang="en">You must either choose a protein, a nucleotid or a user library</text>
</message>
<code proglang="perl">($aa_or_nuc_db eq "protein" and $aadb ne "null") or ( $aa_or_nuc_db eq "user" and defined $userdb) or ($aa_or_nuc_db eq "dna" and $nucdb ne "null") </code>
<code proglang="python">(aa_or_nuc_db == "protein" and aadb != "null") or (aa_or_nuc_db == "user" and userdb is not None) or (aa_or_nuc_db == "dna" and nucdb != "null")</code>
</ctrl>
<comment>
<text lang="en">The program pfsearch tries to identify matches between the input profile and all individual sequences of this library.</text>
</comment>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>aadb</name>
<prompt lang="en">Protein library</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$aa_or_nuc_db eq "protein"</code>
<code proglang="python">aa_or_nuc_db == "protein"</code>
</precond>
<vdef>
<value>null</value>
</vdef>
<xi:include href="../../Local/Services/Programs/Env/protdbs.xml">
<xi:fallback>
<vlist>
<velem undef="1">
<value>null</value>
<label>Choose a database</label>
</velem>
</vlist>
</xi:fallback>
</xi:include>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " <xi:include href="../../Local/Services/Programs/Env/pftools_data.xml" xpointer="xpointer(/db/fasta/text())" />$value" : ""</code>
<code proglang="python">("", " <xi:include href="../../Local/Services/Programs/Env/pftools_data.xml" xpointer="xpointer(/db/fasta/text())" />" + str(value))[value is not None and value != vdef]</code>
</format>
<argpos>100</argpos>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>nucdb</name>
<prompt lang="en">Nucleic library</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$aa_or_nuc_db eq "dna"</code>
<code proglang="python">aa_or_nuc_db == "dna"</code>
</precond>
<vdef>
<value>null</value>
</vdef>
<xi:include href="../../Local/Services/Programs/Env/nucdbs.xml">
<xi:fallback>
<vlist>
<velem undef="1">
<value>null</value>
<label>Choose a database</label>
</velem>
</vlist>
</xi:fallback>
</xi:include>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " <xi:include href="../../Local/Services/Programs/Env/pftools_data.xml" xpointer="xpointer(/db/fasta/text())" />$value" : ""</code>
<code proglang="python">("", " <xi:include href="../../Local/Services/Programs/Env/pftools_data.xml" xpointer="xpointer(/db/fasta/text())" />" + str(value))[value is not None and value != vdef]</code>
</format>
<argpos>100</argpos>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>userdb</name>
<prompt lang="en">User library</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<precond>
<code proglang="perl">$aa_or_nuc_db eq "user"</code>
<code proglang="python">aa_or_nuc_db == "user"</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " $value" : ""</code>
<code proglang="python">("", " "+str(value) )[value is not None]</code>
</format>
<argpos>100</argpos>
</parameter>
<parameter>
<name>psa2msa</name>
<prompt lang="en">Reformat PSA result file to Fasta multiple sequence alignment file?</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " | psa2msa - " : "" </code>
<code proglang="python">( "" , " | psa2msa - " )[ value ]</code>
</format>
<argpos>110</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>control</name>
<prompt lang="en">Control options</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>cutoff</name>
<prompt lang="en">Cut-off level to be used for match selection (-C)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $optimal</code>
<code proglang="python">not optimal</code>
</precond>
<vdef>
<value>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">The value should be the numerical identifier of a cut-off level defined in the profile. The raw or normalized score of this level will then be used to include profile to sequence matches in the output list. If the specified level does not exist in the profile, the next higher (if cut_off is negative) or next lower (if cut_off is positive) level defined is used instead.</text>
</comment>
</parameter>
<parameter>
<name>mode</name>
<prompt lang="en">Normalization mode to use for score (-M)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -M $value" : ""</code>
<code proglang="python">("" , " -M " + str(value))[value is not None]</code>
</format>
<comment>
<text lang="en">The value specifies which normalization mode defined in the profile should be used to compute the normalized scores for profile to sequence matches. This option will override the profile's PRIORITY parameter. If the specified normalization mode does not exist in the profile, an error message will be output to standard error and the search is interrupted.</text>
</comment>
</parameter>
<parameter>
<name>compl</name>
<prompt lang="en">Search the complementary strands of DNA sequences as well (-b) </prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -b" : ""</code>
<code proglang="python">("" , " -b")[ value ]</code>
</format>
</parameter>
<parameter>
<name>raw_score</name>
<prompt lang="en">Use raw scores rather than normalized scores for match selection. Normalized scores will not be listed in the output. (-r) </prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -r" : ""</code>
<code proglang="python">("" , " -r")[ value ]</code>
</format>
</parameter>
<parameter>
<name>unique</name>
<prompt lang="en">Forces DISJOINT=UNIQUE (-u) </prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -u" : ""</code>
<code proglang="python">("" , " -u")[ value ]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output</name>
<prompt lang="en">Output options</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>optimal</name>
<prompt lang="en">Report optimal alignment scores for all sequences regardless of the cut-off value (-a)? </prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -a" : ""</code>
<code proglang="python">("" , " -a")[ value ]</code>
</format>
<comment>
<text lang="en">This option simultaneously forces DISJOINT=UNIQUE.</text>
</comment>
</parameter>
<parameter>
<name>individual_match</name>
<prompt lang="en">Report individual matches for circular profiles (-m)? </prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -m" : ""</code>
<code proglang="python">("" , " -m")[ value ]</code>
</format>
<comment>
<text lang="en">If the profile is circular, each match between a sequence and a profile can be composed of a stretch of individual matches of the profile. By default, pfscan reports only the total matched region. When this option is set, detailed information for each individual match will be output as well.</text>
</comment>
</parameter>
<parameter>
<name>value_hightest_cut_off</name>
<prompt lang="en">Indicate the value of the highest cut-off level exceeded by the match score (-l)? </prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -l" : ""</code>
<code proglang="python">("" , " -l")[ value ]</code>
</format>
</parameter>
<parameter>
<name>char_hightest_cut_off</name>
<prompt lang="en">Indicate by character string of the highest cut-off level exceeded by the match score (-L)? </prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -L" : ""</code>
<code proglang="python">("" , " -L")[ value ]</code>
</format>
<comment>
<text lang="en">The generalized profile format includes a text string field to specify a name for a cut-off level. The -L option causes the program to display the first two characters of this text string (usually something like !, ?, ??, etc.) at the beginning of each match description.</text>
</comment>
</parameter>
<parameter>
<name>Length</name>
<prompt lang="en">Limit profile description length (-d)? </prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $xpsa</code>
<code proglang="python">not xpsa</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -d" : ""</code>
<code proglang="python">("" , " -d")[ value ]</code>
</format>
<comment>
<text lang="en">If this option is set, the description of the profile on the header line will be limited in length. If the match information is longer than the output width specified using option -W, the profile description will not be printed. Else the description will be truncated to fit the -W value.</text>
<text lang="en">By default, the profile description is not truncated. This option can not be used when option -k is set.</text>
</comment>
</parameter>
<parameter>
<name>xpsa</name>
<prompt lang="en">xpsa headers for output (-k)? </prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $Length</code>
<code proglang="python">not Length</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -k" : ""</code>
<code proglang="python">("" , " -k")[ value ]</code>
</format>
<comment>
<text lang="en">When this option is set, all output type will use an xpsa style header line.</text>
<text lang="en">This format uses keyword=value pairs to output alignment parameters. It is useful to transfer information between different sequence alignment tools.</text>
</comment>
</parameter>
<parameter>
<name>listseq</name>
<prompt lang="en">List the sequences of the matched regions as well. The output will be a Pearson/Fasta-formatted sequence library. (-s) </prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -s" : ""</code>
<code proglang="python">("" , " -s")[ value ]</code>
</format>
</parameter>
<parameter>
<name>psa_format</name>
<prompt lang="en">List profile-sequence alignments in pftools PSA format. (-x) </prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -x" : ""</code>
<code proglang="python">("" , " -x")[ value ]</code>
</format>
</parameter>
<parameter>
<name>between</name>
<prompt lang="en">Display alignments between the profile and the matched sequence regions in a human-friendly format. (-y) </prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -y" : ""</code>
<code proglang="python">("" , " -y")[ value ]</code>
</format>
</parameter>
<parameter>
<name>start_end</name>
<prompt lang="en">Indicate starting and ending position of the matched profile range. (-z) </prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -z" : ""</code>
<code proglang="python">("" , " -z")[ value ]</code>
</format>
<comment>
<text lang="en">The latter position will be given as a negative offset from the end of the profile. Thus the range [1,-1] means entire profile.</text>
</comment>
</parameter>
<parameter>
<name>width</name>
<prompt lang="en">Set alignment output width (-W) </prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$listseq or $psa_format or $between </code>
<code proglang="python">listseq or psa_format or between </code>
</precond>
<vdef>
<value>60</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -W $value" : ""</code>
<code proglang="python">("" , " -W "+str(value))[value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">The value specifies how many residues will be output on one line when any of the -s, -x or -y options is set.</text>
</comment>
</parameter>
</parameters>
</paragraph>
</parameters>
</program>
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