2009-04-10  Sandrine Larroude  <slarroud@pasteur.fr>

	* ktreedist.xml: Addition for ktreedist program.
	* gblocks.xml: Addition for gblocks program.

2009-04-09  Herve Menager  <hmenager@pasteur.fr>

	* elp.xml: bugfix: path is fixed.

2009-04-08  Maufrais Corinne  <maufrais@pasteur.fr>

	* abiview.xml, antigenic.xml, backtranambig.xml, backtranseq.xml,
	banana.xml, biosed.xml, btwisted.xml, cai.xml, chaos.xml,
	charge.xml, checktrans.xml, chips.xml, cirdna.xml, codcmp.xml,
	coderet.xml, compseq.xml, cons.xml, cpgplot.xml, cpgreport.xml,
	cusp.xml, cutseq.xml, dan.xml, degapseq.xml, descseq.xml,
	diffseq.xml, digest.xml, distmat.xml, dotmatcher.xml, dotpath.xml,
	dottup.xml, dreg.xml, edialign.xml, einverted.xml, emowse.xml,
	entret.xml, epestfind.xml, eprimer3.xml, equicktandem.xml,
	est2genome.xml, etandem.xml, extractalign.xml, extractfeat.xml,
	extractseq.xml, findkm.xml, freak.xml, fuzznuc.xml, fuzzpro.xml,
	fuzztran.xml, garnier.xml, geecee.xml, getorf.xml,
	helixturnhelix.xml, hmoment.xml, iep.xml, infoalign.xml,
	isochore.xml, lindna.xml, listor.xml, makenucseq.xml,
	makeprotseq.xml, marscan.xml, maskfeat.xml, maskseq.xml,
	matcher.xml, megamerger.xml, merger.xml, msbar.xml, needle.xml,
	newcpgreport.xml, newcpgseek.xml, newseq.xml, notseq.xml,
	nthseq.xml, octanol.xml, oddcomp.xml, palindrome.xml,
	pasteseq.xml, patmatdb.xml, patmatmotifs.xml, pepcoil.xml,
	pepinfo.xml, pepnet.xml, pepstats.xml, pepwheel.xml,
	pepwindow.xml, plotcon.xml, plotorf.xml, polydot.xml, preg.xml,
	prettyplot.xml, prettyseq.xml, primersearch.xml, profit.xml,
	prophecy.xml, prophet.xml, pscan.xml, recoder.xml, redata.xml,
	remap.xml, restover.xml, restrict.xml, revseq.xml,
	seqmatchall.xml, seqret.xml, seqretsplit.xml, showalign.xml,
	showfeat.xml, showorf.xml, showseq.xml, shuffleseq.xml,
	sigcleave.xml, silent.xml, sirna.xml, sixpack.xml, skipseq.xml,
	splitter.xml, stretcher.xml, stssearch.xml, supermatcher.xml,
	syco.xml, tcode.xml, textsearch.xml, tfscan.xml, tmap.xml,
	tranalign.xml, transeq.xml, trimest.xml, trimseq.xml, twofeat.xml,
	union.xml, vectorstrip.xml, water.xml, wobble.xml, wordcount.xml,
	wordfinder.xml, wordmatch.xml, yank.xml: Remove IG format from
	accepted Sequence format.

2009-04-08  Bernard Caudron  <caudron@pasteur.fr>

	* pftools.xml: Add `-v' option, to suppress PROSITE format parsing
	warnings.

2009-04-06  Bertrand Neron  <bneron@pasteur.fr>

	* puzzle.xml: Change the code of outfile , outtree and outdist
	parameters from *.suffix to infile+suffix to avoid useless
	renaming of usertree parameter.

2009-04-03  Maufrais Corinne  <maufrais@pasteur.fr>

        * blast2taxonomy.xml: Output bug fix.

2009-04-02  Bertrand Neron  <bneron@pasteur.fr>

	* neighbor.xml, pars.xml, protpars.xml, dnapars.xml, protdist.xml,
	protpars.xml: The number of data sets must be greater than 1. add
	a ctrl to test that.

2009-03-30  Maufrais Corinne  <maufrais@pasteur.fr>

        * banana.xml, btwisted.xml, charge.xml, digest.xml, emowse.xml,
	epestfind.xml, octanol.xml, pepinfo.xml, pepstats.xml,
	pepwindow.xml, pepwindowall.xml , restover.xml, restrict.xml,
	tcode.xml, tfscan.xml: Change acd 'datafile' parameter from Choice
	to Databox.

2009-03-25  Bertrand Neron  <bneron@pasteur.fr>

	* msa.xml: Change prompt of seqs parameter and remove example
	which is not right.

2009-03-25  Bertrand Neron  <bneron@pasteur.fr>

	* squizz_convert.xml: Add dataformat elements to infile_seq and
	infile_aln parameters.

2009-03-25  Sandrine Larroude  <slarroud@pasteur.fr>

	* mspcrunch.xml: Change of the class of the outfile parameter from
	String to Report.

2009-02-16  Bertrand Neron  <bneron@pasteur.fr>

	* bionj.xml: Add an example in infile parameter.

2009-02-13  Nicolas Joly  <njoly@pasteur.fr>

	* muscle.xml: Assorted perl code fix.

2009-02-09  Bertrand Neron  <bneron@pasteur.fr>

	* hmmcalibrate.xml: hmmcalibrate modify in place the
	hmmprofile. To preserve the input data, the hmmprofile is copied
	before to perform a hmmcalibrate. This operation is specified in
	new hmm_init parameter (the element command is removed).

2009-02-06  Bertrand Neron  <bneron@pasteur.fr>

	* protdist.xml, dnadist.xml: change type of seqboot_out parameter
	from Alignment to setOfAlignment with superclass AbstractText.

	* protpars.xml, dnapars.xml, pars.xml: change the format when
	seqboot is request to preserve the seqboot results as
	seqboot.outfile add a parameter seqboot_out to recover and show to
	the user the seqboot results.

2009-01-30  Bertrand Neron  <bneron@pasteur.fr>

	* fasta.xml: Fix typo in biotype in query parameter Nuucleic ->
	Nucleic.

	* cap3.xml: Fix typo in biotype in contig parameter Nucleiq ->
	Nucleic.

2009-01-27  Bertrand Neron  <bneron@pasteur.fr>

	* protdist.xml: Change ratio parameter type from Integer to Float,
	add a ctrl the value must be >= 0.5, add a comment.

	* dnadist.xml: Change ratio parameter type from Integer to Float,
	add a ctrl the value must be >= 0.0, add a comment.

2009-01-20  Bertrand Neron  <bneron@pasteur.fr>

	* protdist.xml: Parameter gamma ismandatory if gamma_dist in
	["Y","G"] and invariant parameter must be written in paramfile
	instead of command line.

2009-01-20  Bertrand Neron  <bneron@pasteur.fr>

	* bambe.xml: Add biotype Nucleic to data_file.

2009-01-19  Nicolas Joly  <njoly@pasteur.fr>

	* tacg.xml: s/TacgOutput/TacgTextOutput/.

	* blast2mydb.xml: s/Report/Output/ in classes.

	* elp.xml: s/ELPReport/ELPOutput/ in class.

2009-01-16  Nicolas Joly  <njoly@pasteur.fr>

	* wublast2.xml: Fix small typo in text output file class.

	* predator.xml: Fix DSSP input file parameter class.

2009-01-12 Bertrand Neron <bneron@pasteur.fr>

	* bionj.xml: Add an example to the "infile" parameter.

2008-12-10  Nicolas Joly  <njoly@pasteur.fr>

	* blast2mydb.xml: New definition file, that allow a blast search
	against a user provided sequence database.

2008-12-04  Nicolas Joly  <njoly@pasteur.fr>

	* muscle.xml: Do not use empty code, add an empty string instead.

2008-11-28  Nicolas Joly  <njoly@pasteur.fr>

	* fastdnaml.xml: Replace all old/buggy `fastDNAml_boot' calls by a
	new `fastdnaml' script. And kill now unneeded `concattree'.

2008-11-27  Corinne Maufrais  <maufrais@pasteur.fr>

	* drawtree.xml: Update category, display:phylogeny -->
	display:tree.

2008-11-20  Corinne Maufrais  <maufrais@pasteur.fr>

	* consense.xml, drawgram.xml, drawtree.xml, rbvotree.xml,
	tipdate.xml, unroot.xml: Change <category> classification:
	phylogeny:tree is split into --> phylogeny:display and
	phylogeny:tree_analyser and creation of a new diplay:tree
	category.

2008-10-12  Herve Menager  <hmenager@pasteur.fr>

	* mreps.xml, rnainverse.xml: Removed weird character typo that can
	cause xsl processing crashes.

	* comalign.xml, dnadist.xml, dnapars.xml, fasta.xml, garnier.xml,
	hmmbuild.xml, hmmconvert.xml, hmmpfam.xml, mspcrunch.xml,
	muscle.xml, pars.xml, protdist.xml, protpars.xml, seqgen.xml,
	smile.xml, tacg.xml, tipdate.xml: Removed a few contractions from
	the description and comment texts.

2008-10-06  Herve Menager  <hmenager@pasteur.fr>

	* tacg.xml: Removed weird character typo that can cause xsl
	processing crashes.

2008-10-30  Herve Menager  <hmenager@pasteur.fr>

	* fuzznuc.xml, fuzzpro.xml, fuzztran.xml: Class and superclass
	elements have been switched so that the XML validates.

	* stride.xml: Authors and reference elements have been switched so
	that the XML validates.

	* weighbor.xml: The parameter name 'Verbose output' has been
	change to 'verbose' and the prompt to 'Verbose output' to
	eliminate whitespace (not authorized) so that the XML validates
	and the python code evaluation works.

2008-10-28  Herve Menager  <hmenager@pasteur.fr>

	* golden.xml: Typo fix 'accesion->accession'.

2008-10-24  Bertrand Neron  <bneron@pasteur.fr>

	* muscle.xml:
	- Change seqtype option value to auto, protein, dna, rna (as
	  described in user guide protein does not exist).
	- split the parameter to retrieve the results in 3 parameter:
        	muscleReport    if outformat is muscle format
        	htmlReport      if outformat is html
        	AlignmentOutput if outformat is phylip, msf, fasta, clustalw
	- remove unicode char in comment
	- add output format for phylip interleaved and associated comment

2008-10-24  Herve Menager  <hmenager@pasteur.fr>

	* dreg and preg regexps are now infiles and therefore support
	regexps.

2008-10-23  Bertrand Neron  <bneron@pasteur.fr>

	* rnadistance.xml, rnaeval.xml, rnafold.xml, rnainverse.xml:
	Homogenize class to RNAStructure.

2008-10-23  Bertrand Neron  <bneron@pasteur.fr>

	* fitch.xml: Bugfix in global parameter; replace value of
	paramfile element by fitch.params instead of kitsch.params.

2008-10-23  Bertrand Neron  <bneron@pasteur.fr>

	* kitsch.xml: Bugfix in printdata parameter in python code "1\\n" ->
	"1\n".

2008-10-22  Bertrand Neron  <bneron@pasteur.fr>

	* pars.xml: Bugfix in pars.params generation when there is
	multiple_dataset reorganize bootstrap comment to be in same order
	than the bootstrap menu

	* dnadist.xml, protdist.xml, dnapars.xml, protpars.xml: Add
	options in bootstrap parameter (and corresponding comment).

	* dnapars.xml, protpars.xml: Add a control to forbidden that
	replicates*jumble > 100000.

2008-10-22  Bertrand Neron  <bneron@pasteur.fr>

	* protpars.xml, dnapars.xml:
	- add a parameter seqboot_times2jumble in seqboot paragraph to
	  simulate the implicit jumble option when multiple dataset is on.
	- add ctrl in jumble and seqboot to avoid collision between this 2
	  options (the bootstrap option implies multiple dataset in
	  protpars which implies jumble option).
	- add (multiple dataset) in bootsrap prompt.
	- add (one dataset) in jumble prompt.

	* protpars.xml: Add a comment in seqboot.

	* dnapars.xml: Modify the comment in seqboot reformat the example
	in infile.

2008-10-17  Nicolas Joly  <njoly@pasteur.fr>

	* Env/gruppi_env.xml: New env entity file, mandatory for gruppi
	interface.

	* gruppi.xml: Do not use a local entity, but a dummy one instead.

2008-10-16  Herve Menager  <hmenager@pasteur.fr>

	* fuzznuc.xml, fuzzpro.xml, fuzztran.xml: Support regexp special
	  characters, by specifying the patterns as input files. This has
	  the further advantage of being compatible with EMBOSS capability
	  of handling more than one pattern (bneron, njoly, hmenager).

2008-09-30  Nicolas Joly  <njoly@pasteur.fr>

	* *.xml: Rename *Report classes to *Output.

	* hmmbuild.xml, mfold.xml: Switch from Text to AbstractText in
	superclass.

	* pftools.xml, prose.xml, scan_for_matches.xml: Do some
	consistency renaming for patterns.

	* rnadistance.xml: Rename StructureAlignment to
	RnadistanceAlignment.

	* dssp.xml: Rename DsspOut to DsspOutput.

	* blast2taxonomy.xml, boxshade.xml, mfold.xml, psiblast.xml,
	psort.xml, tacg.xml, toppred.xml: Use consistent class naming for
	HTML output files.

2008-09-30  Bertrand Neron  <bneron@pasteur.fr>

	* mreps.xml: Change class of parameter xmlout from XML to
	MrepsXmlReport.

2008-09-30  Bertrand Neron  <bneron@pasteur.fr>

	* rnafold.xml: Change class of parameter outfile from
	RNAFoldSequence to RnaFoldSequence change class of parameter seq
	from RNAStruct to RnaStruct.

2008-09-30  Nicolas Joly  <njoly@pasteur.fr>

	* comalign.xml, dnapars.xml, fitch.xml, lvb.xml, pars.xml,
	protpars.xml: Fix typos (Alignement -> Alignment).

	* xpound.xml: Fix typo, and class renaming for consistency
	(xxOutfile -> xxOutput).

2008-09-30  Bertrand Neron  <bneron@pasteur.fr>

	* pratt.xml: Change class of distfile parameter from
	DistanceMatrix to PhylipDistanceMatrix.

2008-09-30  Bertrand Neron  <bneron@pasteur.fr>

	* blast2.xml, phiblast.xml, psiblast.xml, wublast2.xml: Rename
	class BlastXMLReport to BlastXmlReport.

2008-09-30  Bertrand Neron  <bneron@pasteur.fr>

	* blast2.xml, html4blast.xml, phiblast.xml, wublast2.xml: Rename
	class BlastHTMLReport to BlastHtmlReport.

2008-09-30  Bertrand Neron  <bneron@pasteur.fr>

	* abiview.xml, banana.xml, boxshade.xml, chaos.xml, charge.xml,
	cirdna.xml, combat.xml, cpgplot.xml, dan.xml, dotmatcher.xml,
	dotpath.xml, dottup.xml, drawgram.xml, drawtree.xml,
	epestfind.xml, findkm.xml, freak.xml, genscan.xml, gff2ps.xml,
	hmoment.xml, iep.xml, isochore.xml, lindna.xml, mfold.xml,
	octanol.xml, pepinfo.xml, pepnet.xml, pepwheel.xml,
	pepwindowall.xml, pepwindow.xml, plotcon.xml, plotorf.xml,
	polydot.xml, prettyplot.xml, rnaalifold.xml, rnacofold.xml,
	rnadistance.xml, rnaduplex.xml, rnafold.xml, rnalfold.xml,
	rnapdist.xml, rnaplfold.xml, rnasubopt.xml, syco.xml, tacg.xml,
	tcode.xml, tmap.xml, wobble.xml, xpound.xml: Rename class
	Postscript to PostScript.

2008-09-30  Nicolas Joly  <njoly@pasteur.fr>

	* hmm*.xml, wise2.xml: Rename HmmProfile to HmmTextProfile.

	* hmmbuild.xml, hmmconvert.xml: Rename HmmProfileBin to
	HmmBinProfile.

	* hmmbuild.xml: Consistently use `Hmm' (lowercase) in classes.

2008-09-30  Bertrand Neron  <bneron@pasteur.fr>

	* seqgen.xml: Bugfix in rateAll format each rate are float thus the
	string format is not %d but %f.

2008-09-30  Bertrand Neron  <bneron@pasteur.fr>

	* seqgen.xml: Fix bug in comment/text element of parameter rate1
	and paragraph rate: add lang attribute.

2008-09-30  Bertrand Neron  <bneron@pasteur.fr>

	*seqgen.xml: Fix bug in format of rateAll:
	- in python rate1 rate2 rate3 are variables not string
	- in perl invalid syntax
	- add a comment in paragraph rate to advertise that this option is
	  useful only with nucleotides models of substitution.

2008-09-29  Bertrand Neron  <bneron@pasteur.fr>

	* fasta.xml: Change outfile parameter class from FastaReport to
	FastaTextReport, html_outfile parameter class from Html to
	FastaHtmlReport.

	* mview.xml: Change fasta parameter class from FastaReport to
	FastaTextReport.

2008-09-29  Bertrand Neron  <bneron@pasteur.fr>

	* clique.xml, mix.xml, pars.xml: Change DiscreteCharMatrix to
	PhylipDiscreteCharMatrix.

2008-09-29  Bertrand Neron  <bneron@pasteur.fr>

	* bionj.xml, dnadist.xml, fitch.xml, kitsch.xml, neighbor.xml,
	protdist.xml, quicktree.xml, weighbor.xml: Change class
	DistanceMatrix to PhylipDistanceMatrix.

2008-09-29  Bertrand Neron  <bneron@pasteur.fr>

	* rnadistance.xml: Change the class of psfiles parameter from
	AbstractText to Binary.

2008-09-22  Nicolas Joly  <njoly@pasteur.fr>

	* mview.xml: Kill `in_p' parameter, the input file format is now
	set in each input parameter. And add `force=1' to the alignment
	input, to be able to handle CLUSTAL format with sequence numbers.

2008-09-22  Bertrand Neron  <bneron@pasteur.fr>

	* tipdate.xml: param change_confidence: add a precond, the control
	must be evaluated only if change_confidence is True.

2008-09-12  Nicolas Joly  <njoly@pasteur.fr>

	* golden.xml: Remove command path attribute.

	* golden.xml, gruppi.xml: Remove XML stylesheet.

2008-09-11  Nicolas Joly  <njoly@pasteur.fr>

	* boxshade.xml: Kill the `env' entity reference which does not
	exists.

	* *.xml: Consistently use SYSTEM identifier for DOCTYPE
	declaration.

	* tipdate.xml: Remove unneeded memory parameter (which do only
	pollute program output).

2008-09-10  Nicolas Joly  <njoly@pasteur.fr>

	* dialign.xml: Make it validate, by moving a precond a correct
	position.

2008-09-09  Herve Menager  <hmenager@pasteur.fr>

	* extractfeat.xml: Change two parameter names and their evaluation
	line, because there seems to be a problem with the evaluation when
	a parameter name is "value".  so 'tag' becomes 'tag_name' and
	'value' becomes 'tag_value'.

2008-09-05  Bertrand Neron  <bneron@pasteur.fr>

	* tipdate.xml:
	- param change_rate_estim change vdef from +w to off add ctrl if
	w+ (tip_date or tip_date_specified).
	- param change_confidence add ctrl -iw option can only be used
	with Variable Rate Tip Date Model (+w).

2008-08-29  Bertrand Neron  <bneron@pasteur.fr>

	* boxshade.xml: boxshade doesn't support clustal v2.0 format;
	force the conversion in clustal 1.8 add force="1" attribute to
	acceptedDataFormats element of alignment parameter.

2008-08-21  Bertrand Neron  <bneron@pasteur.fr>

	* dnapars.xml protpars.xml pars.xml neighbor.xml: Add lang
	attribute to text element in comment element in outgroup
	parameter.

2008-08-21  Bertrand Neron  <bneron@pasteur.fr>

	* dnapars.xml protpars.xml pars.xml neighbor.xml: Add comment in
	outgroup option.

2008-08-18  Bertrand Neron  <bneron@pasteur.fr>

	* codonw.xml: Typo in doclink tutorial url.

2008-08-05  Bertrand Neron  <bneron@pasteur.fr>

	* abiview.xml: Modify the typing of "infile" parameter from
	<class>Binary</class> to <class>AbiTraceFile</class>
	<superclass>Binary</superclass>.

2008-08-04  Bertrand Neron  <bneron@pasteur.fr>

	* codonw: Add 2 externals docklinks,
	http://codonw.sourceforge.net/Readme.html
	http://codonw.sourceforge.net/Tutorial.html

2008-07-31  Bertrand Neron  <bneron@pasteur.fr>

	* for all phylip xml: Update the version tag from 3.65 to 3.67.

	* dnadist.xml: Change matrix_form parameter to Choice to integrate
	new option : "human_redable" appeared with Phylip v3.67.

2008-07-04  Bertrand Neron  <bneron@pasteur.fr>

	* muscle.xml: Add a doclink.

2008-07-04  Bertrand Neron  <bneron@pasteur.fr>

	* muscle.xml: Add the xml of muscle in repository.

2008-06-25  Bertrand Neron  <bneron@pasteur.fr>

	* dialign.xml: Add a parameter fasta_alignment to recover fasta
	alignment in right type.

2008-06-23  Nicolas Joly  <njoly@pasteur.fr>

	* xpound.xml: Add missing input file name for xpscript command.

2008-06-11  Bertrand Neron  <bneron@pasteur.fr>

	* hmmbuild.xml, hmmcalibrate.xml,hmmconvert.xml, hmmemit.xml:
	Small typo in category, s/builting/building/.

2008-06-10  Nicolas Joly  <njoly@pasteur.fr>

	* hmmfetch.xml: Small typo, s/pfamprag/pfamfrag/.

2008-06-06  Nicolas Joly  <njoly@pasteur.fr>

	* Version 1.0 released.

