/var/lib/mobyle/programs/mspcrunch.xml is in mobyle-programs 5.1.1-1.
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>
<name>mspcrunch</name>
<version>2.5</version>
<doc>
<title>MSPcrunch</title>
<description>
<text lang="en">A BLAST post-processing filter</text>
</description>
<authors>Sonnhammer, Durbin</authors>
<doclink>http://bioweb2.pasteur.fr/docs/mspcrunch/MSPcrunch2.pdf</doclink>
<homepagelink>http://sonnhammer.sbc.su.se/MSPcrunch.html</homepagelink>
<sourcelink>http://sonnhammer.sbc.su.se/download/software/MSPcrunch+Blixem/</sourcelink>
</doc>
<category>database:search:display</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>mspcrunch</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"MSPcrunch"</code>
<code proglang="python">"MSPcrunch"</code>
</format>
<argpos>0</argpos>
</parameter>
<paragraph>
<name>input_options</name>
<prompt lang="en">Input Options</prompt>
<argpos>1</argpos>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>blast_output</name>
<prompt lang="en">BLAST output File</prompt>
<type>
<datatype>
<class>BlastTextReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" "+str(value)</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter>
<name>force_blastp</name>
<prompt lang="en">Force Blastp mode (default Blastx) (-p)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -p" : "" </code>
<code proglang="python">( "" , " -p" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>force_blastn</name>
<prompt lang="en">Force Blastn mode (default Blastx) (-n)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -n" : "" </code>
<code proglang="python">( "" , " -n" )[ value ]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>analyse_options</name>
<prompt lang="en">Control options</prompt>
<argpos>1</argpos>
<parameters>
<parameter>
<name>gapped</name>
<prompt lang="en">Make gapped alignment of ungapped-MSP contigs (-G)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -G" : "" </code>
<code proglang="python">( "" , " -G" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>cov_limit</name>
<prompt lang="en">Set coverage limit (-l)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -l $value" : "" </code>
<code proglang="python">( "" , " -l "+str(value) )[ value is not None and value !=vdef]</code>
</format>
<comment>
<text lang="en">0 = No coverage rejection</text>
</comment>
</parameter>
<parameter>
<name>old_cutoff</name>
<prompt lang="en">Use old step cutoffs for adjacency instead of the new continuous system. (-O)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -O" : "" </code>
<code proglang="python">( "" , " -O" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>dont_reject</name>
<prompt lang="en">Don't reject any MSPs (-w)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -w" : "" </code>
<code proglang="python">( "" , " -w" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>report_rejected</name>
<prompt lang="en">Report only rejected MSPs (-r)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -r" : "" </code>
<code proglang="python">( "" , " -r" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>threshold_id</name>
<prompt lang="en">Reject all matches with less than this % identity (-I)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -I $value" : "" </code>
<code proglang="python">( "" , " -I " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>threshold_length</name>
<prompt lang="en">Reject all matches with length less than this value (-L)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -L $value" : "" </code>
<code proglang="python">( "" , " -L " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>expect</name>
<prompt lang="en">Reject all matches with E-value higher than this value (-e)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -e $value" : ""</code>
<code proglang="python">( "" , " -e " + str(value))[ value is not None ]</code>
</format>
</parameter>
<!-- core dumped
<parameter>
<name>matrix</name>
<prompt lang="en">Scoring matrix (PAM or BLOSUM) (-m)</prompt>
<type>
<datatype>
<class>ScoringMatrix</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl"> ($value) ? " -m $value" : ""</code>
<code proglang="python">( "" , " -m " + str(value) )[ value is not None ]</code>
</format>
</parameter>
-->
<parameter>
<name>query</name>
<prompt lang="en">Read in query seq (for rereading .seqbl files) (-Q)</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">(defined $value)? " -Q $query" : "" </code>
<code proglang="python">( "" , " -Q " + str(value) )[ value is not None ]</code>
</format>
</parameter>
<parameter>
<name>whole_contig</name>
<prompt lang="en">Coverage limitation requires whole contig to be covered (always for Blastp) (-a)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -a" : "" </code>
<code proglang="python">( "" , " -a" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>hits_to_self</name>
<prompt lang="en">Accept hits to self (-s)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -s" : "" </code>
<code proglang="python">( "" , " -s" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>no_hits_to_earlier</name>
<prompt lang="en">Ignore hits to earlier seqnames (for All-vs-All) (-A)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -A" : "" </code>
<code proglang="python">( "" , " -A" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>stats_without_X</name>
<prompt lang="en">Recalculate percentage identity, ignoring X residues. (-j)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -j" : "" </code>
<code proglang="python">( "" , " -j" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>stats_without_end</name>
<prompt lang="en">Recalculate percentage identity, ignoring mismatches at ends. (-J)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -J" : "" </code>
<code proglang="python">( "" , " -J" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>silent_mutations</name>
<prompt lang="en">Do Statistics of Silent mutations (only cDNA!) (-S)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -S" : "" </code>
<code proglang="python">( "" , " -S" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>matrix_stats</name>
<prompt lang="en">Print statistics on used matrices (-E)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -E" : "" </code>
<code proglang="python">( "" , " -E" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>all_expected</name>
<prompt lang="en">Print all Expected scores (default only when positive) (-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>line_length</name>
<prompt lang="en">Line length of Wrapped alignment (-W)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -W $value" : "" </code>
<code proglang="python">( "" , " -W " +str(value) )[ value is not None ]</code>
</format>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>output_options</name>
<prompt lang="en">Output Options</prompt>
<argpos>1</argpos>
<parameters>
<parameter isstdout="1">
<name>outfile</name>
<prompt lang="en">Result file</prompt>
<type>
<datatype>
<class>Report</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"mspcrunch.out" </code>
<code proglang="python">"mspcrunch.out" </code>
</filenames>
</parameter>
<parameter>
<name>big_pict</name>
<prompt lang="en">Big Picture output (-P)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -P" : "" </code>
<code proglang="python">( "" , " -P" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>matches_one_line</name>
<prompt lang="en">For Big Picture output, force all matches to the same subject on one line (-F)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$big_pict</code>
<code proglang="python">big_pict</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -F" : "" </code>
<code proglang="python">( "" , " -F" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>sfs</name>
<prompt lang="en">Produce SFS output (-H)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -H" : ""</code>
<code proglang="python">( "" , " -H" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>seqbl</name>
<prompt lang="en">Produce seqbl output for Blixem (-q)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -q" : "" </code>
<code proglang="python">( "" , " -q" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>wublast_numbered</name>
<prompt lang="en">Indicate query insertions with numbers (For seqbl output from Wublast) (-N)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$seqbl</code>
<code proglang="python">seqbl</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -N" : "" </code>
<code proglang="python">( "" , " -N" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>ace</name>
<prompt lang="en">Produce .ace output (for ACEDB 4) (-4)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -4" : "" </code>
<code proglang="python">( "" , " -4" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>dont_mirror</name>
<prompt lang="en">Don't mirror (i.e. print the subject object) in ACE4 format (-M)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$ace</code>
<code proglang="python">ace</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -M" : "" </code>
<code proglang="python">( "" , " -M" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>exblx</name>
<prompt lang="en">Produce exblx output (for easy parsing) (-x)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -x" : "" </code>
<code proglang="python">( "" , " -x" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>exbldb</name>
<prompt lang="en">Produce exbldb output (as exblx with query names) (-d)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -d" : "" </code>
<code proglang="python">( "" , " -d" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>fasta</name>
<prompt lang="en">Produce fasta output (unaligned, for mult.alignm.) (-2)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -2" : "" </code>
<code proglang="python">( "" , " -2" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>three_frame</name>
<prompt lang="en">Print 3 frame translation (blastn only) (-3)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -3" : "" </code>
<code proglang="python">( "" , " -3" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>footer</name>
<prompt lang="en">Print footer with parameters and stats (-f)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -f" : "" </code>
<code proglang="python">( "" , " -f" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>percentage_id</name>
<prompt lang="en">Print percentage identity (seqbl output only) (-i)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$seqbl</code>
<code proglang="python">seqbl</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -i" : "" </code>
<code proglang="python">( "" , " -i" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>stats</name>
<prompt lang="en">Output coverage stats?</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
</parameter>
<parameter isout="1">
<name>stats_file</name>
<prompt lang="en">Coverage stats outputfile</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="perl">$stats</code>
<code proglang="python">stats</code>
</precond>
<format>
<code proglang="perl">($value) ? " -o mspcrunch.stats" : "" </code>
<code proglang="python">( "" , " -o mspcrunch.stats" )[ value is not None ]</code>
</format>
<filenames>
<code proglang="perl">"mspcrunch.stats"</code>
<code proglang="python">"mspcrunch.stats"</code>
</filenames>
</parameter>
<parameter>
<name>domainer</name>
<prompt lang="en">Produce output for Domainer (trim overlaps) (-D)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -D" : "" </code>
<code proglang="python">( "" , " -D" )[ value ]</code>
</format>
</parameter>
</parameters>
</paragraph>
</parameters>
</program>
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