/var/lib/mobyle/programs/blast2taxoclass.xml is in mobyle-programs 5.1.2-1.
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 xmlns:xi="http://www.w3.org/2001/XInclude">
<name>blast2taxoclass</name>
<version>1.0</version>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/blastTaxoAnalysis_package.xml"/>
<doc>
<title>blast2taxoclass</title>
<description>
<text lang="en">Blast filtering with taxonomic hierarchy information</text>
</description>
<authors>C. Maufrais</authors>
</doc>
<category>database:search:filter</category>
<command>blast2taxoclass</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>infile</name>
<prompt lang="en">Blast output file</prompt>
<type>
<datatype>
<class>BlastTextReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<format>
<code proglang="perl">" -i $value"</code>
<code proglang="python">" -i " + str(value)</code>
</format>
<argpos>20</argpos>
</parameter>
<parameter issimple="1">
<name>blastfilter</name>
<prompt lang="en">Find taxonomic classification of:</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>M</value>
</vdef>
<vlist>
<velem>
<value>M</value>
<label>best hit</label>
</velem>
<velem>
<value>F</value>
<label>most frequent hit</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value) ? " -$value" : ""</code>
<code proglang="python">" -" + str(value)</code>
</format>
</parameter>
<parameter>
<name>nbofhit</name>
<prompt lang="en">Number of hsp to consider (-x)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10</value>
</vdef>
<format>
<code proglang="perl">(defined $value) ? " -x $value" : ""</code>
<code proglang="python">("", " -x " + str(value) )[value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">0: all hsp </text>
</comment>
</parameter>
<paragraph>
<name>taxonomicfilter</name>
<prompt lang="en">Taxonomic hierarchy filter option</prompt>
<parameters>
<parameter issimple="1">
<name>position</name>
<prompt lang="en">Relative position in taxonomic hierarchy (-p)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -p $value" : ""</code>
<code proglang="python">("", " -p " + str(value) )[value is not None]</code>
</format>
<ctrl>
<message>
<text lang="en">Choose only one of taxonomic hierarchy filter option: Relative position, Taxonomic rank or Taxonomic name.</text>
</message>
<code proglang="perl">(defined $position and (not defined $taxonomic_name and not defined $rank))</code>
<code proglang="python">(position is not None and (taxonomic_name is None and rank is None)) or (taxonomic_name is not None and (position is None and rank is None)) or (rank is not None and (taxonomic_name is None and position is None)) </code>
</ctrl>
<comment>
<text lang="en">zero means: root of taxonomy, higher value: leaf or near </text>
</comment>
</parameter>
<parameter issimple="1">
<name>taxonomic_name</name>
<prompt lang="en">Taxonomic Name (-n)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -n $value" : ""</code>
<code proglang="python">("", " -n " + str(value).replace(' ','_') )[value is not None]</code>
</format>
<ctrl>
<message>
<text lang="en">Choose only one of taxonomic hierarchy filter option: Relative position, Taxonomic rank or Taxonomic name.</text>
</message>
<code proglang="perl">(defined $position and (not defined $taxonomic_name and not defined $rank))</code>
<code proglang="python">(position is not None and (taxonomic_name is None and rank is None)) or (taxonomic_name is not None and (position is None and rank is None)) or (rank is not None and (taxonomic_name is None and position is None)) </code>
</ctrl>
</parameter>
<parameter issimple="1">
<name>rank</name>
<prompt lang="en">Taxonomic rank name (-r)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label></label>
</velem>
<velem>
<value>superkingdom</value>
<label>superkingdom</label>
</velem>
<velem>
<value>kingdom</value>
<label>kingdom</label>
</velem>
<velem>
<value>subkingdom</value>
<label>subkingdom</label>
</velem>
<velem>
<value>superphylum</value>
<label>superphylum</label>
</velem>
<velem>
<value>phylum</value>
<label>phylum</label>
</velem>
<velem>
<value>subphylum</value>
<label>subphylum</label>
</velem>
<velem>
<value>superclass</value>
<label>superclass</label>
</velem>
<velem>
<value>class</value>
<label>class</label>
</velem>
<velem>
<value>subclass</value>
<label>subclass</label>
</velem>
<velem>
<value>infraclass</value>
<label>infraclass</label>
</velem>
<velem>
<value>superorder</value>
<label>superorder</label>
</velem>
<velem>
<value>order</value>
<label>order</label>
</velem>
<velem>
<value>suborder</value>
<label>suborder</label>
</velem>
<velem>
<value>infraorder</value>
<label>infraorder</label>
</velem>
<velem>
<value>parvorder</value>
<label>parvorder</label>
</velem>
<velem>
<value>superfamily</value>
<label>superfamily</label>
</velem>
<velem>
<value>family</value>
<label>family</label>
</velem>
<velem>
<value>subfamily</value>
<label>subfamily</label>
</velem>
<velem>
<value>tribe</value>
<label>tribe</label>
</velem>
<velem>
<value>subtribe</value>
<label>subtribe</label>
</velem>
<velem>
<value>genus</value>
<label>genus</label>
</velem>
<velem>
<value>subgenus</value>
<label>subgenus</label>
</velem>
<velem>
<value>species_group</value>
<label>species_group</label>
</velem>
<velem>
<value>species_subgroup</value>
<label>species_subgroup</label>
</velem>
<velem>
<value>species</value>
<label>species</label>
</velem>
<velem>
<value>subspecies</value>
<label>subspecies</label>
</velem>
<velem>
<value>varietas</value>
<label>varietas</label>
</velem>
<velem>
<value>forma</value>
<label>forma</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value) ? " -r $value" : ""</code>
<code proglang="python">("", " -r " + str(value) )[value is not None]</code>
</format>
<ctrl>
<message>
<text lang="en">Choose only one of taxonomic hierarchy filter option: Relative position, Taxonomic rank or Taxonomic name.</text>
</message>
<code proglang="perl">(defined $position and (not defined $taxonomic_name and not defined $rank))</code>
<code proglang="python">(position is not None and (taxonomic_name is None and rank is None)) or (taxonomic_name is not None and (position is None and rank is None)) or (rank is not None and (taxonomic_name is None and position is None)) </code>
</ctrl>
<comment>
<text lang="en">If Taxonomic rank is not defined for one hit, it is not treated.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output</name>
<prompt lang="en">Output option</prompt>
<parameters>
<parameter>
<name>blastout</name>
<prompt lang="en">Blast output file(s) sort/split by specific taxonomic hierarchy (-b)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -b" : ""</code>
<code proglang="python">("" , " -b") [value]</code>
</format>
</parameter>
<parameter>
<name>queryout</name>
<prompt lang="en">Query name write in file(s) sort/split by specific taxonomic hierarchy (-q)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -q" : ""</code>
<code proglang="python">("" , " -q") [value]</code>
</format>
</parameter>
<parameter>
<name>fastaExtract</name>
<prompt lang="en">Extraction of fasta sequences.</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<ctrl>
<message>
<text lang="en">Query name write in file must be checked and query sequences must be done.</text>
</message>
<code proglang="perl">$fastaExtract == 1 and $queryout == 1 and defined $query_seq</code>
<code proglang="python">(fastaExtract and (queryout and query_seq is not None)) or (not fastaExtract)</code>
</ctrl>
<comment>
<text lang="en">Extract fasta sequence, matching specified taxonomic filter, from file containing query sequences witch are used to made blast.</text>
</comment>
</parameter>
<parameter>
<name>query_seq</name>
<prompt lang="en">Query sequences witch are used to made blast.</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
<card>1,n</card>
</type>
<precond>
<code proglang="perl">defined $fastaExtract and defined $queryout</code>
<code proglang="python">fastaExtract and queryout</code>
</precond>
<format>
<code proglang="perl">(defined $value)? " && extractfasta -i $query *.qry": ""</code>
<code proglang="python">(""," && extractfasta -i "+ str(value) + " *.qry") [value is not None]</code>
</format>
<argpos>100</argpos>
</parameter>
<parameter isstdout="1">
<name>outfile</name>
<prompt>Output file</prompt>
<type>
<datatype>
<class>Blast2taxoclassReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"blast2taxoclass.out"</code>
<code proglang="python">"blast2taxoclass.out"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>blastoutfile</name>
<prompt>Blast output file(s)</prompt>
<type>
<datatype>
<class>BlastTextReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">defined $blastout</code>
<code proglang="python">blastout</code>
</precond>
<filenames>
<code proglang="perl">"*.blast"</code>
<code proglang="python">"*.blast"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>queryoutfile</name>
<prompt>Query name file</prompt>
<type>
<datatype>
<class>QueryNameReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">defined $queryout</code>
<code proglang="python">queryout</code>
</precond>
<filenames>
<code proglang="perl">"*.qry"</code>
<code proglang="python">"*.qry"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>fastafile</name>
<prompt>Fasta file</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $fastaExtract</code>
<code proglang="python">fastaExtract</code>
</precond>
<filenames>
<code proglang="perl">"*.fasta"</code>
<code proglang="python">"*.fasta"</code>
</filenames>
</parameter>
</parameters>
</paragraph>
</parameters>
</program>
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