Mercurial > repos > dcorreia > noisy
changeset 4:fe4a6ac63fa2 draft
Uploaded
| author | dcorreia |
|---|---|
| date | Tue, 15 Mar 2016 05:57:50 -0400 |
| parents | 8f0b1876daee |
| children | b77cbee86c50 |
| files | noisy.xml test-data/aln.fasta test-data/aln_out.fas tool_dependencies.xml |
| diffstat | 4 files changed, 45 insertions(+), 173 deletions(-) [+] |
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--- a/noisy.xml Tue Mar 15 05:53:11 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,167 +0,0 @@ -<tool id="noisy" name="Noisy" version="1.5.12.1"> - <description>Cleaning aligned sequences</description> - <requirements> - <requirement type="package" version="1.5.12">noisy</requirement> - </requirements> - <command><![CDATA[ - noisy $input - - #if $sequence.seqtype == 'cfg' : - ## Automatic sequence detection - ## read an info file to choose which option set - #set $info = open( str($input_info) ).read() - #if 'dna' in $info: - --seqtype D - #else if 'protein' in $info : - --seqtype P - #end if - - #else : - --seqtype $sequence.seqtype - #end if - - --cutoff $cutoff - --distance $distance - #if $usematrix.matrix == "true": - --matrix $usematrix.matrixfile - #end if - #if $missingchar.setmissingchar == "true": - --missing $missingchar.chars - #end if - --ordering - #if $orderingmethode.ordering == "rand": - RAND[,$orderingmethode.randpermut] - #else if $orderingmethode.ordering == "list": - $orderingmethode.randpermutlist - #else: - $orderingmethode.ordering - #end if - - $constant - $gap - - --shuffles $shuffles - --smooth $smooth - --silent - - ]]> - </command> - <inputs> - <param name="input" type="data" format="fasta" label="Source file" help="Fasta format" /> - <conditional name="sequence"> - <param name="seqtype" type="select" label="Sequence Coding"> - <option value="D">DNA</option> - <option value="P">Protein</option> - <option value="R">RNA</option> - <option value="cfg">Config file</option> - </param> - <when value="D"></when> - <when value="P"></when> - <when value="R"></when> - <when value="auto"> - <param name="input_info" type="data" format="txt" label="info" help="Precompute file containning sequence description (dna or protein)" /> - </when> - </conditional> - <param name="cutoff" type="float" value="0.8" min="0" max="1" label="cut-off [ 0-1 ]" help="Columns with a score below FLOAT are removed from the output alignment." /> - <param name="distance" type="select" label="Distance methode used by NeighbotNet"> - <option value="HAMMING">HAMMING</option> - <option value="GTR">GTR</option> - </param> - <conditional name="usematrix"> - <param name="matrix" type="boolean" truevalue="true" falsevalue="" checked="False" label="Use matrix file" help="default is calculate distances with nnet"/> - <when value=""/> - <when value="true"> - <param name="matrixfile" format="text" type="data" label="matrix file"/> - </when> - </conditional> - <conditional name="missingchar"> - <param name="setmissingchar" type="boolean" truevalue="true" falsevalue="" checked="False" label="Set list of missing chars" /> - <when value=""/> - <when value="true"> - <param name="chars" type="text" label="Missing chars list"/> - </when> - </conditional> - <conditional name="orderingmethode"> - <param name="ordering" type="select" display="radio" label="Choose ordering method"> - <option value="nnet">NeighborNet</option> - <option value="qnet">QNet</option> - <option value="rand">Sample INT random permutation</option> - <option value="list">List of index MSA ordering</option> - <option value="all">All permutations</option> - </param> - <when value="nnet"/> - <when value="qnet"/> - <option value="all"/> - <when value="rand"> - <param name="randpermut" type="integer" value="1000" label="random permutation"/> - </when> - <when value="list"> - <param name="randpermutlist" type="text" label="Comma-seperated string of INT"/> - </when> - </conditional> - <param name="constant" type="boolean" truevalue="" falsevalue="--noconstant" checked="True" label="Constant columns in output alignment" /> - <param name="gap" type="boolean" truevalue="" falsevalue="--nogap" checked="True" label="Count gap symbol as character state"/> - <param name="smooth" type="integer" value="1" min="0" max="1000" label="Running average over INT columns" help="Calculate a running average over the reliability score of INT columns and use this smoothed values to remove unreliable columns from the MAS.s" /> - <param name="shuffles" type="integer" value="0" min="0" max="1000" label="Perform INT random shuffles per column of the MSA"/> - </inputs> - <outputs> - <data name="output1" format="fasta" label="Noisy Cleaned sequencies" from_work_dir="*_out.fas" /> - <data name="output2" format="eps" label="Noisy Cleaned sequencies image" from_work_dir="*_typ.eps" /> - <data name="output3" format="txt" label="Noisy Cleaned sequencies information" from_work_dir="*_sta.gr" /> - </outputs> - <tests> - <test> - <param name="input" value="aln.fasta" /> - <output name="output1" file="aln_out.fas" /> - </test> - </tests> - -<help> -<![CDATA[ -Usage:: - - noisy [OPTIONS] MultiFastaAlignment - -Options:: - - --cutoff FLOAT Set cutoff value to FLOAT. Columns with a score below FLOAT are removed from the output alignment. - (default is >0.80<) - --distance STRING Distance methode used by NeighbotNet. - (default is >HAMMING< [HAMMING|GTR]) - -h, --help Print usage message for noisy. - --matrix FILE Use distance matrix for NeighbotNet from FILE. - (default is >calculate distances with nnet<) - --missing STRING Set list of missing characters to STRING. - (default is >N<) - --nogap Don't count gap symbol as character state. - (default is >0<) - --noconstant Ignore constant columns in output alignment. - (default is >0<) - --ordering STRING - Choose ordering method. - (default is >nnet<) - nnet NeighborNet - qnet QNet algorithm is O(n^4) both in time and memory, be careful when you use this option. - rand[,INT] sample INT random permutation. With rand a random sample of all possible orderings of the TAXA can be specified for which the reliability score is calculated - (default is >1000<) - INT,INT,... provide ordering explicitly as comma-seperated list of TAXA indices in the range (e.g 3,0,4,1,2 as ordering for the 5 TAXA in the input MSA). - all all permutations, If all is used than for all possible permutations of the TAXA the reliability score is calculated (Note that for more than 8 TAXA this can become rather time consuming!). - - --shuffles INT Perform INT random shuffles per column. - (default is >0<) - -s, --silent Turn off status bar - (default is >0<) - --smooth INT Running avarage over INT columns. - (default is >1<) - --seqtype CHAR Set sequence type of input alignment to CHAR - (default is >D<) [D=DNA, P=Protein, R=RNA] - -v, --verbose Verbose mode. Causes noisy to print debugging - messages about its progress. -]]> -</help> - <citations> - <citation type="doi">10.1186/1748-7188-3-7</citation> - <citation type="doi">10.1093/molbev/msl180</citation> - <citation type="doi">10.1093/molbev/msh018s</citation> - </citations> -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aln.fasta Tue Mar 15 05:57:50 2016 -0400 @@ -0,0 +1,35 @@ +>TestSequence1 +ERNECFLKHKDDDPNLPPVVKPEPEALCTAFQENNNKFLENYLYEVARRHPYFYGPELLY +YVKQ--YKAILTECCQAACCQAADKATCLAPKAKVLKEKLLASSAKQRHKCASIQKFGER +AFKAWSIARLSQRFPKADFMDLSKLVTDLSKIHKECCHGDLLECADDREDLAKYV---QD +SFSSKLKECCDKPLLEKSHCISELENDDLPNDLPSITTDFVEDKDVCKLLNYKEAKDVFL +GTFLYEYSRRHPEYAVSLLLRIAKGYEATLERCCATDDAHACYSKVFDELQPLVDEPQ-- +KLMKRNCELFENLGAYGFQNALIIRYTKKMPQVSTPTLLVISKELANMGNKCCTLPESKR +>TestSequence2 +ERADCFASHRDDNPGFPLMVRPPVDELCASYQADAQMFAGKYLYEVARRYPYFYAPELLY +YAQKLLYKDALAEC-----CSAADKAACLTPKIDDLKESVMTSGAKQRFKCAGIEKFGER +AFKAWAVARLSQKFPNADFAEISKIVTDLTKINKECCHGDLLECADDRVELGKYMCDNKD +SISSKLGKCCEKPLLEKGHCIAELERDDMPADLSPIEADFVEDKEVCK--NYAEAKDVFL +GTFLYELSRRHPEYSVVMLLRLAKGYEAVLEKCCATGDPPACYAKVFDELKPLIDEPQ-- +NLVKHNCELYGNLQEYGFQNALLIRYTKKMPQ---PTLVEVSRNLGKVGTKCCSLAEGER +>TestSequence3 +ERNECFLSHKDDSPDLPKL-KPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLY +YANK--YNGVFQEC-----CQAEDKGACLLPKIETMREKVLTSSARQRLRCASIQKFGER +ALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQD +TISSKLKECCDKPLLEKSHCIAEVEKDAVPENLPPLTADFAEDKDVCK--NYQEAKDAFL +GSFLYEYSRRHPE-YVLLRLALLKEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQ-- +NLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGTRCCTKPESER +>TestSequence4 +ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF +FAKR--YKAAFTEC-----CQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGER +AFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQD +SISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCK--NYAEAKDVFL +GMFLYEYARRHPRESVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQLL +NLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKR +>TestSequence5 +ERNECFLQHKDDNPGFGQLVTPEADAMCTAFHENEQRFLGKYLYEIARRHPYFYAPELLY +YAEE--YKGVFTEC-----CEAADKAACLTPKVDALREKVLASSAKERLKCASLQKFGER +AFKAWSVARLSQKFPKAEFAEISKLVTDLAKIHKECCHGDLLECADDRADLAKYICENQD +SISTKLKECCGKPVLEKSHCISEVERDELPADLPPLAVDFVEDKEVCK--NYQEAKDVFL +GTFLYEYSRRHPS-SVSLLLRLAKEYEATLEKCCATDDPPACYAHVFDEFKPLVEEPH-- +NLVKTNCELFEKLGEYGFQNALLVRYTKKVPQVSTPTLVEVSRSLGKVGSKCCTHPEAER \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aln_out.fas Tue Mar 15 05:57:50 2016 -0400 @@ -0,0 +1,10 @@ +>TestSequence1 +ERNCFHDDPPCNFNYLYEARRPYFYPELLYKECCADKCLPKSARCAKFGERAKAWARLSQFPKAFKVTDLKHECCHGDLLECADDRLKY-DSKLCCKPLEKHCIEEDPDLDFEKVCKYEAKDFLGFLYERRHPVLKYELECCADCYVFDLEPKLKCLYFQALRYTKPQPTLSLNGCCER +>TestSequence5 +ERNCFHDDPPCNFKYLYEARRPYFYPELLYKECCADKCLPKSARCAKFGERAKAWARLSQFPKAFKVTDLKHECCHGDLLECADDRLKYNDSKLCCKPLEKHCIEEDPDLDFEKVCKYEAKDFLGFLYERRHPVLKYELECCADCYVFDLEPNLKCLYFQALRYTKPQPTLSLKGCCER +>TestSequence2 +ERACFHDDPPCDFKYLYEARRPYFYPELLYKECCADKCLPKSARCAKFGERAKAWARLSQFPNAFKVTDLKNECCHGDLLECADDRLKYNDSKLCCKPLEKHCIEEDPDLDFEKVCKYEAKDFLGFLYERRHPVLKYELECCADCYVFDLEPNLKCLYFQALRYTKPQPTLSLKGCCER +>TestSequence3 +ERNCFHDDPPCDFKYLYEARRPYFYPELLYNECCADKCLPKSARCAKFGERAKAWARLSQFPKAFKVTDLKHECCHGDLLECADDRLKYNDSKLCCKPLEKHCIEEDPNLDFEKVCKYEAKDFLGFLYERRHPVLKYELECCADCYVFDLEPNLKCLYFQALRYTKPQPTLSLKGCCER +>TestSequence4 +ERNCFHDDPPCNFKYLYEARRPYFYPELLYKECCADKCLPKSARCAKFGERAKAWARLSQFPKAFKVTDLKHECCHGDLLECADDRLKYNDSKLCCKPLEKHCIEEDPDLDFEKVCKYEAKDFLGFLYERRHPVLKYELECCADCYVFDLEPNLKCLYFQALRYTKPQPTLSLKGCCER
--- a/tool_dependencies.xml Tue Mar 15 05:53:11 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="noisy" version="1.5.12"> - <repository changeset_revision="143f88be27b7" name="package_noisy_1_5_12" owner="dcorreia" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> \ No newline at end of file