/var/lib/mobyle/programs/blast2genoclass.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>blast2genoclass</name>
<version>1.0</version>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/blastTaxoAnalysis_package.xml"/>
<doc>
<title>blast2genoclass</title>
<description>
<text lang="en">One-line description of Blast program filtering</text>
</description>
<authors>C. Maufrais</authors>
</doc>
<category>database:search:filter</category>
<command>blast2genoclass</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 $value"</code>
<code proglang="python">" -i " + str(value)</code>
</format>
<argpos>20</argpos>
</parameter>
<parameter issimple="1">
<name>blastfilter</name>
<prompt lang="en">Filter the one-line description of Blast program with:</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>Null</value>
</vdef>
<vlist>
<velem undef="1">
<value>Null</value>
<label></label>
</velem>
<velem>
<value>M</value>
<label>best e-value</label>
</velem>
<velem>
<value>F</value>
<label>most frequent description</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value ne vdef) ? " -$value" : ""</code>
<code proglang="python">("", " -" + str(value))[value != vdef]</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>
<parameter issimple="1">
<name>genomic_name</name>
<prompt lang="en">Filter the one-line description of Blast program with user name (-p)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -p $value" : ""</code>
<code proglang="python">("", " -p " + str(value).replace(' ','_') )[value is not None]</code>
</format>
<ctrl>
<message>
<text lang="en">Choose only one of the one-line description filter option: User name or not.</text>
</message>
<code proglang="perl">(defined $blastfilter and (not defined $genomic_name)) or (defined $genomic_name and (not defined $blastfilter))</code>
<code proglang="python">(blastfilter is not None and (genomic_name is None)) or (genomic_name is not None and (blastfilter is None)) </code>
</ctrl>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>taxonomic_name</name>
<prompt lang="en">Filter the hit of Blast with Taxonomic hierarchy name (-n)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -n $value" : ""</code>
<code proglang="python">("", " -n " + str(value).replace(' ','_') )[value is not None]</code>
</format>
</parameter>
<paragraph>
<name>output</name>
<prompt lang="en">Output option</prompt>
<parameters>
<parameter>
<name>verboseall</name>
<prompt lang="en">Report detailed results matching "Description filter option" for all blast (-v)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -v" : ""</code>
<code proglang="python">("" , " -v") [value]</code>
</format>
<comment>
<text lang="en">In "res4individualBlast.txt" file, for all input blast, are details: </text>
<text lang="en">For all matching "Description filter option":</text>
<text lang="en">- query name, (query letter): percentage of matching description</text>
<text lang="en">and for all corresponding hits:</text>
<text lang="en">- Database sequence's species, accession number and letters</text>
<text lang="en">- Hsp description</text>
</comment>
</parameter>
<parameter>
<name>verbose</name>
<prompt lang="en">Detailed report for database sequence(s) matching "Description filter option" (-V)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -V" : ""</code>
<code proglang="python">("" , " -V") [value]</code>
</format>
<comment>
<text lang="en">In "res4allBlast.txt" file, for the best database sequence(s), are details: </text>
<text lang="en">For database sequence matching "Description filter option":</text>
<text lang="en">- Database sequence's species, accession number, letters and description</text>
<text lang="en">- Number of query matching this sequence.</text>
<text lang="en">- Query name, (letters)</text>
<text lang="en">and for all corresponding hsp:</text>
<text lang="en">- Hsp description</text>
</comment>
</parameter>
<parameter>
<name>option</name>
<prompt lang="en">Hsp(s) selection (-m)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<vlist>
<velem>
<value>0</value>
<label>All hsps</label>
</velem>
<velem>
<value>1</value>
<label>Only compatible hsps</label>
</velem>
<velem>
<value>2</value>
<label>Simple overlaps are possible</label>
</velem>
<velem>
<value>3</value>
<label>Global overlaps on database sequence(s) are possible</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value ne vdef) ? " -m $value" : ""</code>
<code proglang="python">("", " -m " + str(value))[value != vdef]</code>
</format>
</parameter>
<parameter>
<name>align</name>
<prompt lang="en">Produce alignment: database sequence matching "Description filter option" vs queries (-a)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<vlist>
<velem undef="1">
<value>0</value>
<label></label>
</velem>
<velem>
<value>1</value>
<label>hsps blast and database sequence reference alignment: hsp merged in pairwise alignment</label>
</velem>
<velem>
<value>2</value>
<label>hsps blast and database sequence reference alignment: hsp in multiple alignment</label>
</velem>
<velem>
<value>3</value>
<label>hsps blast and database sequence reference alignment: hsp in multiple alignment and consensus</label>
</velem>
<velem>
<value>4</value>
<label>part of queries (hsp) and database sequence reference alignment: queries merged in pairwise alignment</label>
</velem>
<velem>
<value>5</value>
<label>part of queries (hsp) and database sequence reference alignment: queries in multiple alignment</label>
</velem>
<velem>
<value>6</value>
<label>part of queries (hsp) and database sequence reference alignment: queries in multiple alignment and consensus</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value ne vdef)? " -a $value" : ""</code>
<code proglang="python">("" , " -a " +str(value)) [value != vdef]</code>
</format>
<comment>
<text lang="en">For 1,2,3 hsps alignments (Sbjt and Query) are re-aligned on the reference sequence extract from database.</text>
<text lang="en">For 4,5,6 part of queries corresponding to hsps are re-aligned on the reference sequence extract from database.</text>
</comment>
</parameter>
<parameter>
<name>picture</name>
<prompt lang="en">Produce graphical alignment summary images: database sequence matching "Description filter option" vs queries (-g)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -g" : ""</code>
<code proglang="python">("" , " -g") [value]</code>
</format>
</parameter>
<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">($value)? " -b" : ""</code>
<code proglang="python">("" , " -b") [value]</code>
</format>
</parameter>
<parameter>
<name>hspSeq</name>
<prompt lang="en">Extract Hsp(s) fragment from Query sequence(s) (-Q)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -Q" : ""</code>
<code proglang="python">("" , " -Q") [value]</code>
</format>
<!-- <ctrl>
<message>
<text lang="en">Query sequences must be done.</text>
</message>
<code proglang="perl">defined $query_seq</code>
<code proglang="python">query_seq is not None</code>
</ctrl> -->
</parameter>
<parameter>
<name>queryout</name>
<prompt lang="en">Query name write in file(s) sort/split by specific taxonomic hierarchy (-q)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -q" : ""</code>
<code proglang="python">("" , " -q") [value]</code>
</format>
</parameter>
<parameter>
<name>besthitseq</name>
<prompt lang="en">Report database sequence(s) matching option in fasta file (-s)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -s" : ""</code>
<code proglang="python">("" , " -s") [value]</code>
</format>
</parameter>
<parameter>
<name>fastaExtract</name>
<prompt lang="en">Extraction of fasta sequences.</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<ctrl>
<message>
<text lang="en">Query name write in file must be checked and query sequences must be done.</text>
</message>
<code proglang="perl">$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>
</parameter>
<parameter ishidden="1">
<name>query_seq_run1</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 $hspSeq and defined $query_seq</code>
<code proglang="python">hspSeq and query_seq</code>
</precond>
<format>
<code proglang="perl">(defined $value)? " -f $query_seq": ""</code>
<code proglang="python">(""," -f "+ str(query_seq)) [query_seq is not None]</code>
</format>
</parameter>
<parameter ishidden="1">
<name>query_seq_run2</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 and defined $query_seq</code>
<code proglang="python">fastaExtract and queryout and query_seq</code>
</precond>
<format>
<code proglang="perl">(defined $value)? " && extractfasta -i $query_seq *.qry": ""</code>
<code proglang="python">(""," && extractfasta -i "+ str(query_seq) + " *.qry") [query_seq 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">"blast2genoclass.out"</code>
<code proglang="python">"blast2genoclass.out"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>pictureout</name>
<prompt>Graphical output</prompt>
<type>
<datatype>
<class>Picture</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">defined $picture</code>
<code proglang="python">picture</code>
</precond>
<filenames>
<code proglang="perl">"*.png"</code>
<code proglang="python">"*.png"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>alignout</name>
<prompt>Alignment</prompt>
<type>
<datatype>
<class>GenoClasAln</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">defined $align</code>
<code proglang="python">align</code>
</precond>
<filenames>
<code proglang="perl">"*.aln"</code>
<code proglang="python">"*.aln"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>verboseoutall</name>
<prompt>Verbose output file for all blast</prompt>
<type>
<datatype>
<class>VerboseReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">defined $verboseall</code>
<code proglang="python">verboseall</code>
</precond>
<filenames>
<code proglang="perl">"res4individualBlast.txt"</code>
<code proglang="python">"res4individualBlast.txt"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>verboseout</name>
<prompt>Verbose output file for database sequence(s)</prompt>
<type>
<datatype>
<class>VerboseReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">defined $verbose</code>
<code proglang="python">verbose</code>
</precond>
<filenames>
<code proglang="perl">"res4allBlast.txt"</code>
<code proglang="python">"res4allBlast.txt"</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>besthitseqfile</name>
<prompt>Database sequence(s) fasta file</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<precond>
<code proglang="perl">defined $besthitseq</code>
<code proglang="python">besthitseq</code>
</precond>
<filenames>
<code proglang="perl">"*.dbfasta"</code>
<code proglang="python">"*.dbfasta"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>fastafile</name>
<prompt>Fasta file</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<precond>
<code proglang="perl">defined $fastaExtract or defined $hspSeq</code>
<code proglang="python">fastaExtract or hspSeq</code>
</precond>
<filenames>
<code proglang="perl">"*.fasta"</code>
<code proglang="python">"*.fasta"</code>
</filenames>
</parameter>
</parameters>
</paragraph>
</parameters>
</program>
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