#Last update: 11/06/2008
#
#
# When you make changes to anything in the sdk, you can use this file
# and the ToolTest class to make sure you haven't broken any tools
# that were running.  Therefore, everything in here *must* run:
# if you add parameters for a tool you are testing and you aren't
# finished, or it doesn't work, please comment them out before
# committing this file.  Also be sure to add any required entries
# in test.properties and the corresponding tool data dir.
#
# Tests that are *slow*, for example, that won't complete in 15 min
# or less, should be added to the end of this file, after the
# "These are Slow tools" comment.  That way, we can easily run just
# the "fast" tests when we want to by creating a temporary version
# of this file and removing or commenting out the slow tests.
#
#The parameters for adding your tool here SHOULD be generated in the following way:
#first look at the document \q\documents\for_developers\Releasing_a_new_tool.doc
#in the ngbw svn repository.
#
#Using that document, learn how to run the command <ant clean generate Test>
#
#this will produce output files entitles testInputfiles.properties and test.properties.
#
#you can cut the new tool information for test.properties and testInfile.properties 
#and paste it here; HOWEVER: if there are more the one input files required; those must be
#added by hand. the required/preferred syntax is 
#
#TOOLNAME.infilename_= examples/tooltest/TOOLNAME/TOOLNAME_in(x).txt
#where (x) represents the the input number, if more than one input is required.
#for example: if two inputs are required the input would be:
#
#TOOLNAME.infile1name_= examples/tooltest/TOOLNAME/TOOLNAME_in.txt
#TOOLNAME.infile2name_= examples/tooltest/TOOLNAME/TOOLNAME_in2.txt
#
# There are non-conforming legacy paths in the doc below, these will be eliminated
# if mamiller ever get bored enough
#
#######################################################################################
#
#    Please dont be a TOOL!
#
#	 Add your tool in alphabetical order 
#
#
#######################################################################################
# ALIGN
#
#
ALIGN.query1_= examples/tooltest/ALIGN/alignn1_in.txt
ALIGN.query2_= examples/tooltest/ALIGN/alignn2_in.txt
#
#

# BL2SEQ
#
#
BL2SEQ.first_sequence_= examples/tooltest/BLAST2SEQ/blast2seqn1_in.txt
BL2SEQ.second_sequence_= examples/tooltest/BLAST2SEQ/blast2seqn2_in.txt
#
#
#

# BLAST2
#
#
BLAST2.query_= examples/tooltest/BLAST2/blast2_in.txt
#
#
#

# BLASTN
#
#
BLASTN.query_= examples/tooltest/BLASTN/blastn_in.txt
#
#
#

# BLASTP
#
#
BLASTP.query_= examples/tooltest/BLASTP/blastp_in.txt
#
#
#

# BLASTX
#
#
BLASTX.query_= examples/tooltest/BLASTX/blastx_in.txt
#
#
#

# BLIMPS
#
#
BLIMPS.sequence_file_= examples/tooltest/BLIMPS/blimps_seq_in.txt
#
#
#

# BOXSHADE
#
#
BOXSHADE.alignment_= examples/tooltest/BOXSHADE/boxshadep_in.aln
#
#
#

# CLIQUE
#
#
CLIQUE.infile_= examples/tooltest/CLIQUE/clique_in.phy
#
#
#

# CLUSTALW
#
#
CLUSTALW.infile_= examples/tooltest/CLUSTALW/clustalw_seq_in.fasta
#
#
#

# CLUSTALW_DIST
#
#
CLUSTALW_DIST.infile_= examples/tooltest/CLUSTALW_DIST/CLUSTALW_DIST_in.txt
#
#
#

# CLUSTALW_N
#
#
CLUSTALW_N.infile_= examples/tooltest/CLUSTALW_N/CLUSTALW_N_in.txt
#
#
<!-- fix me -->
# CLUSTALW_P
#
#
CLUSTALW_P.infile_= examples/tooltest/CLUSTALW_P/CLUSTALW_P_in.txt
#
#
#
<!-- fix me -->

# CLUSTALW_PROFILE
#
#
CLUSTALW_PROFILE.profile1_= examples/tooltest/CLUSTALW_PROFILE/CLUSTALW_PROFILE_in.txt
CLUSTALW_PROFILE.profile2_= examples/tooltest/CLUSTALW_PROFILE/CLUSTALW_PROFILE_in2.txt
CLUSTALW_PROFILE.usetree1_= examples/tooltest/CLUSTALW_PROFILE/CLUSTALW_PROFILE_in3.txt
CLUSTALW_PROFILE.usetree2_= examples/tooltest/CLUSTALW_PROFILE/CLUSTALW_PROFILE_in4.txt
#
#
#

# CLUSTALW_TREE
#
#
CLUSTALW_TREE.infile_= examples/tooltest/CLUSTALW_TREE/CLUSTALW_TREE_in.txt
#
#
#

# CONSENSE
#
#
CONSENSE.infile_= src/main/java/org/ngbw/examples/tooltest/CONSENSE/CONSENSE_in.txt
#
#
#

# DEGAPSEQ
#
#
DEGAPSEQ.sequence_= src/main/java/org/ngbw/examples/tooltest/DEGAPSEQ/DEGAPSEQ_in.txt
#
#
#

# DNADIST
#
#
DNADIST.infile_= src/main/java/org/ngbw/examples/tooltest/DNADIST/DNADIST_in.txt
#
#
#

# DNAPARS
#
#
DNAPARS.infile_= src/main/java/org/ngbw/examples/tooltest/DNAPARS/DNAPARS_in.txt
#
#
#

# DOLLOP
#
#
DOLLOP.infile_= src/main/java/org/ngbw/examples/tooltest/DOLLOP/DOLLOP_in.txt
#
#
#

# DRAWGRAM
#
#
DRAWGRAM.treefile_= examples/tooltest/DRAWGRAM/drawgram_in.dnd
#
#
#

# DRAWTREE
#
#
DRAWTREE.treefile_= examples/tooltest/DRAWTREE/drawtree_in.dnd
#
#
#

# DSSP
#
#
DSSP.pdbfile_= examples/tooltest/DSSP/dssp_in.pdb
#
#
#

# FASTA_N
#
#
FASTA_N.query_= examples/tooltest/FASTA_N/FASTA_N_in.txt
#
#
#

# FASTA_P
#
#
FASTA_P.query_= examples/tooltest/FASTA_P/FASTA_P_in.txt
#
#
#

# FASTX
#
#
FASTX.query_= examples/tooltest/FASTX/FASTX_in.txt
#
#
#

# FASTY
#
#
FASTY.query_= examples/tooltest/FASTY/FASTY_in.txt
#
#
#

# FINGERPRINTSCAN
#
#
FINGERPRINTSCAN.sequence_= examples/tooltest/FINGERPRINTSCAN/fingerprintscan_in.txt
#
#
#

# FITCH
#
#
FITCH.infile_= examples/tooltest/FITCH/fitch_in.pdm
#
#
#

# FORMATVALIDATOR
#
#
FORMATVALIDATOR.infile_= examples/tooltest/FORMATVALIDATOR/FORMATVALIDATOR_in.txt
#
#
#

# GARLI
#
#
GARLI.infile_= examples/tooltest/GARLI/GARLI_in.txt
#
#
#

# HELIXTURNHELIX
#
#
HELIXTURNHELIX.sequence_= examples/tooltest/HELIXTURNHELIX/helixturnhelix_in.txt
#
#
#

# HMMPFAM
#
#
HMMPFAM.seqfile_= examples/tooltest/HMMPFAM/hmmpfam_in.txt
#
#
#

# KITSCH
#
#
KITSCH.infile_= examples/tooltest/KITSCH/kitsch_in.pdm
#
#
#

# LALIGN
#
#
LALIGN.query1_= examples/tooltest/LALIGN/lalign1_in.txt
LALIGN.query2_= examples/tooltest/LALIGN/lalign2_in.txt
#
#

# MAFFT
#
#
MAFFT.infile_= examples/tooltest/MAFFT/MAFFT_in.txt
#
#
#

# MFOLD
#
#
MFOLD.SEQ_= examples/tooltest/MFOLD/mfold_in.txt
#
#
#

# MIX
#
#
MIX.infile_= examples/tooltest/MIX/mix_in.phy
MIX.mixture_file_= examples/tooltest/MIX/mixture.txt
MIX.tree_file_= examples/tooltest/MIX/mix_usertree.txt
#
#
#

# MRBAYES
#
#
MRBAYES.infile_= examples/tooltest/MRBAYES/MRBAYES_in.txt
#
#
#

# MSA
#
#
MSA.seqs_= examples/tooltest/MSA/msa_nucl_in.txt
#
#
#

# MUSCLE
#
#
MUSCLE.infile_= examples/tooltest/MUSCLE/MUSCLE_in.txt
#
#
#

# MVIEW_ALIG
#
#
MVIEW_ALIG.alig_= examples/tooltest/MVIEW_ALIG/mview_alig_in.txt
#
#
#

# MVIEW_BLAST
#
#
MVIEW_BLAST.blast_output_= examples/tooltest/MVIEW_BLAST/mview_blast_in.txt
#
#
#

# NEIGHBOR
#
#
NEIGHBOR.infile_= examples/tooltest/NEIGHBOR/neighbor_in.pdm
#
#
#

# NEW_TOOL
#
#
NEW_TOOL.infile_= src/main/java/org/ngbw/examples/tooltest/NEW_TOOL/NEW_TOOL_in.txt
#
#
#

# PARS
#
#
PARS.infile_= examples/tooltest/PARS/pars_in.phy
#
#
#

# PAUP
#
#
PAUP.infile_= examples/tooltest/PAUP/PAUP_in.txt
#
#
#

# PEPINFO
#
#
PEPINFO.sequence_= examples/tooltest/PEPINFO/pepinfo_in.txt
#
#
#

# PEPSTATS
#
#
PEPSTATS.sequence_= examples/tooltest/PEPSTATS/pepstats_in.txt
#
#
#

# PEPWINDOW
#
#
PEPWINDOW.sequence_= examples/tooltest/PEPWINDOW/pepwindow_in.txt
#
#
#

# PFSCAN
#
#
PFSCAN.seqfile_= examples/tooltest/PFSCAN/pfscan_in.txt
#
#
#

# PFSEARCH
#
#
PFSEARCH.profile_= examples/tooltest/PFSEARCH/pfsearch_matrix_in.txt
#
#
#

# PHYML
#
#
PHYML.alignment_= examples/tooltest/PHYML/phyml_in.aln
PHYML.user_tree_file_= examples/tooltest/PHYML/phyml_guidetree.dnd
#
#
#

# POY
#
#
POY.infile1_= examples/tooltest/POY/POY_in.txt
#
#
#

# PPSEARCH
#
#
PPSEARCH.inputfile_= examples/tooltest/PPSEARCH/ppsearch_in.txt
#
#
#

# PROBALIGN
#
#
PROBALIGN.infile_= examples/tooltest/PROBALIGN/PROBALIGN_in.txt
#
#
#

# PROSEARCH
#
#
PROSEARCH.protein_= examples/tooltest/PROSEARCH/prosearch_in.txt
#
#
#

# PROTDIST
#
#
PROTDIST.infile_= examples/tooltest/PROTDIST/protdist_in.phy
#
#
#

# PROTEUS
#
#
PROTEUS.sequence_= examples/tooltest/PROTEUS/PROTEUS_in.txt
#
#
#

# PROTPARS
#
#
PROTPARS.infile_= examples/tooltest/PROTPARS/protpars_in.phy
#
#
#

# PRSS
#
#
PRSS.query1_= examples/tooltest/PRSS/prssn1_in.txt
PRSS.query2_= examples/tooltest/PRSS/prssn2_in.txt
#
#
#

# PSIBLAST
#
#
PSIBLAST.query_= examples/tooltest/PSIBLAST/psiblast_in.txt
#
#
#

# PSIPRED
#
#
PSIPRED.sequence_= examples/tooltest/PSIPRED/psipred_in.txt
#
#
#

# RAXMLHPC
#
#
RAXMLHPC.infile_= examples/tooltest/RAXMLHPC/RAXMLHPC_in.txt
#
#
#

# RESTRICT
#
#
RESTRICT.sequence_= examples/tooltest/RESTRICT/RESTRICT_in.txt
#
#
#

# REVSEQ
#
#
REVSEQ.sequence_= examples/tooltest/REVSEQ/revseq_in.txt
#
#
#

# RID3PAUP
#
# 
RID3PAUP.infile_= examples/tooltest/RID3PAUP/RID3PAUP_in.txt
#
#
#

# RID3RAXML
#
# 
RID3RAXML.infile_= examples/tooltest/RID3RAXML/RID3RAXML_in.txt
#
#
#

# RPSBLAST
#
#
RPSBLAST.query_= examples/tooltest/RPSBLAST/rpsblast_in.txt
#
#
#

# SAPS
#
#
SAPS.seq_= examples/tooltest/SAPS/saps_in.txt
#
#
#

# SEQBOOT
#
#
SEQBOOT.infile_= examples/tooltest/SEQBOOT/seqboot_in.txt
#
#
#

# SIXPACK
#
#
SIXPACK.sequence_= examples/tooltest/SIXPACK/sixpack_in.txt
#
#
#

# SLEEP IS NOT INCLUDED
#
#
#SLEEP.infile_= src/main/java/org/ngbw/examples/tooltest/SLEEP/SLEEP_in.txt
#
#
#

# SPIDEY
#
#
SPIDEY.first_sequence_= examples/tooltest/SPIDEY/SPIDEY_in.txt
SPIDEY.query2_= examples/tooltest/SPIDEY/SPIDEY_in2.txt
#
#
#

# SSEARCH_N
#
#
SSEARCH_N.query_= examples/tooltest/SSEARCH/ssearch_in2.txt
#
#
#

# SSEARCH_P
#
#
SSEARCH_P.query_= examples/tooltest/SSEARCH/ssearch_in1.txt
#
#
#

# TACG
#
#
TACG.sequence_= examples/tooltest/TACG/tacg_in.txt
#
#
#

# TBLASTN
#
#
TBLASTN.query_= examples/tooltest/BLAST2/tblastn_in.txt
#
#
#

# TBLASTX
#
#
TBLASTX.query_= examples/tooltest/TBLASTX/TBLASTX_in.txt
#
#
#

# TFASTA
#
#
TFASTA.query_= examples/tooltest/TFASTA/TFASTA_in.txt
#
#
#

# TFASTX
#
#
TFASTX.query_= examples/tooltest/TFASTX/TFASTX_in.txt
#
#
#

# TFASTY
#
#
TFASTY.query_= examples/tooltest/TFASTY/TFASTY_in.txt
#
#
#

# TMAP
#
#
TMAP.sequences_= examples/tooltest/TMAP/tmap_in.aln
#
#
#

# UNROOT
#
#
UNROOT.treefile_= examples/tooltest/UNROOT/unroot_clustal_in.dnd
#
#
#