| Next changeset 1:3b7dde5c3ec4 (2016-03-23) |
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Commit message:
Imported from capsule None |
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added:
noisy.xml test-data/aln.fasta test-data/aln_out.fas tool_dependencies.xml |
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| diff -r 000000000000 -r ab2cf9c6c4f1 noisy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/noisy.xml Tue Mar 15 06:07:50 2016 -0400 |
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| b'@@ -0,0 +1,167 @@\n+<tool id="noisy" name="Noisy" version="1.5.12.1">\n+ <description>Cleaning aligned sequences</description>\n+ <requirements>\n+ <requirement type="package" version="1.5.12">noisy</requirement>\n+ </requirements>\n+ <command><![CDATA[ \n+ noisy $input\n+ \n+ #if $sequence.seqtype == \'cfg\' :\n+\t ## Automatic sequence detection\n+\t ## read an info file to choose which option set \n+\t #set $info = open( str($input_info) ).read()\n+\t #if \'dna\' in $info:\n+\t --seqtype D\n+\t #else if \'protein\' in $info :\n+\t --seqtype P\n+\t #end if\n+\t \n+ #else :\n+ --seqtype $sequence.seqtype\n+ #end if \n+ \n+ --cutoff $cutoff\n+ --distance $distance\n+ #if $usematrix.matrix == "true":\n+ --matrix $usematrix.matrixfile\n+ #end if\n+ #if $missingchar.setmissingchar == "true":\n+ --missing $missingchar.chars\n+ #end if\n+ --ordering\n+ #if $orderingmethode.ordering == "rand":\n+ RAND[,$orderingmethode.randpermut]\n+ #else if $orderingmethode.ordering == "list":\n+ $orderingmethode.randpermutlist\n+ #else:\n+ $orderingmethode.ordering\n+ #end if\n+ \n+ $constant\n+ $gap\n+ \n+ --shuffles $shuffles\n+ --smooth $smooth\n+ --silent\n+ \n+ ]]>\n+ </command>\n+\t<inputs>\n+\t\t<param name="input" type="data" format="fasta" label="Source file" help="Fasta format" />\n+\t\t<conditional name="sequence">\n+\t\t\t<param name="seqtype" type="select" label="Sequence Coding">\n+\t\t\t\t<option value="D">DNA</option>\n+\t\t\t\t<option value="P">Protein</option>\n+\t\t\t\t<option value="R">RNA</option>\n+\t\t\t\t<option value="cfg">Config file</option>\n+\t\t\t</param>\n+\t\t\t<when value="D"></when>\n+\t\t\t<when value="P"></when>\n+\t\t\t<when value="R"></when>\n+\t\t\t<when value="auto">\n+ <param name="input_info" type="data" format="txt" label="info" help="Precompute file containning sequence description (dna or protein)" />\n+ </when>\t\n+\t\t</conditional> \n+\t\t<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." />\n+\t\t<param name="distance" type="select" label="Distance methode used by NeighbotNet">\n+\t\t <option value="HAMMING">HAMMING</option>\n+ <option value="GTR">GTR</option>\n+ </param>\n+ <conditional name="usematrix">\n+ <param name="matrix" type="boolean" truevalue="true" falsevalue="" checked="False" label="Use matrix file" help="default is calculate distances with nnet"/>\n+ <when value=""/>\n+ <when value="true">\n+ <param name="matrixfile" format="text" type="data" label="matrix file"/>\n+ </when>\n+ </conditional>\n+ <conditional name="missingchar">\n+ <param name="setmissingchar" type="boolean" truevalue="true" falsevalue="" checked="False" label="Set list of missing chars" />\n+ <when value=""/>\n+ <when value="true">\n+ <param name="chars" type="text" label="Missing chars list"/>\n+ </when>\n+ </conditional>\n+ <conditional name="orderingmethode">\n+\t <param name="ordering" type="select" display="radio" label="Choose ordering method">\n+\t <option value="nnet">NeighborNet</option>\n+\t <option value="qnet">QNet</option>\n+\t <option value="rand">Sample INT random permutation</option>\n+\t <option value="list">List of'..b'1000" label="random permutation"/>\n+ </when>\n+ <when value="list">\n+ <param name="randpermutlist" type="text" label="Comma-seperated string of INT"/>\n+ </when>\n+ </conditional>\n+ <param name="constant" type="boolean" truevalue="" falsevalue="--noconstant" checked="True" label="Constant columns in output alignment" />\n+ <param name="gap" type="boolean" truevalue="" falsevalue="--nogap" checked="True" label="Count gap symbol as character state"/>\n+ <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" />\n+ <param name="shuffles" type="integer" value="0" min="0" max="1000" label="Perform INT random shuffles per column of the MSA"/>\n+\t</inputs>\n+\t<outputs>\n+\t\t<data name="output1" format="fasta" label="Noisy Cleaned sequencies" from_work_dir="*_out.fas" />\n+\t\t<data name="output2" format="eps" label="Noisy Cleaned sequencies image" from_work_dir="*_typ.eps" />\n+\t\t<data name="output3" format="txt" label="Noisy Cleaned sequencies information" from_work_dir="*_sta.gr" />\n+\t</outputs>\n+\t<tests>\n+ <test>\n+\t <param name="input" value="aln.fasta" />\n+\t <output name="output1" file="aln_out.fas" /> \n+ </test>\n+\t</tests>\n+\t\n+<help>\n+<![CDATA[ \n+Usage::\n+\n+ noisy [OPTIONS] MultiFastaAlignment\n+\n+Options::\n+\n+ --cutoff FLOAT Set cutoff value to FLOAT. Columns with a score below FLOAT are removed from the output alignment.\n+ (default is >0.80<)\n+ --distance STRING Distance methode used by NeighbotNet.\n+ (default is >HAMMING< [HAMMING|GTR])\n+ -h, --help Print usage message for noisy.\n+ --matrix FILE Use distance matrix for NeighbotNet from FILE.\n+ (default is >calculate distances with nnet<)\n+ --missing STRING Set list of missing characters to STRING.\n+ (default is >N<)\n+ --nogap Don\'t count gap symbol as character state.\n+ (default is >0<)\n+ --noconstant Ignore constant columns in output alignment.\n+ (default is >0<)\n+ --ordering STRING\n+ Choose ordering method.\n+ (default is >nnet<)\n+ nnet NeighborNet\n+ qnet QNet algorithm is O(n^4) both in time and memory, be careful when you use this option.\n+ 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\n+ (default is >1000<)\n+ 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).\n+ 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!).\n+\n+ --shuffles INT Perform INT random shuffles per column.\n+ (default is >0<)\n+ -s, --silent Turn off status bar\n+ (default is >0<)\n+ --smooth INT Running avarage over INT columns.\n+ (default is >1<)\n+ --seqtype CHAR Set sequence type of input alignment to CHAR\n+ (default is >D<) [D=DNA, P=Protein, R=RNA]\n+ -v, --verbose Verbose mode. Causes noisy to print debugging\n+ messages about its progress.\n+]]>\n+</help>\n+ <citations>\n+ <citation type="doi">10.1186/1748-7188-3-7</citation>\n+ <citation type="doi">10.1093/molbev/msl180</citation>\n+ <citation type="doi">10.1093/molbev/msh018s</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r ab2cf9c6c4f1 test-data/aln.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aln.fasta Tue Mar 15 06:07:50 2016 -0400 |
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| @@ -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 |
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| diff -r 000000000000 -r ab2cf9c6c4f1 test-data/aln_out.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aln_out.fas Tue Mar 15 06:07:50 2016 -0400 |
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| @@ -0,0 +1,10 @@ +>TestSequence1 +ERNCFHDDPPCNFNYLYEARRPYFYPELLYKECCADKCLPKSARCAKFGERAKAWARLSQFPKAFKVTDLKHECCHGDLLECADDRLKY-DSKLCCKPLEKHCIEEDPDLDFEKVCKYEAKDFLGFLYERRHPVLKYELECCADCYVFDLEPKLKCLYFQALRYTKPQPTLSLNGCCER +>TestSequence5 +ERNCFHDDPPCNFKYLYEARRPYFYPELLYKECCADKCLPKSARCAKFGERAKAWARLSQFPKAFKVTDLKHECCHGDLLECADDRLKYNDSKLCCKPLEKHCIEEDPDLDFEKVCKYEAKDFLGFLYERRHPVLKYELECCADCYVFDLEPNLKCLYFQALRYTKPQPTLSLKGCCER +>TestSequence2 +ERACFHDDPPCDFKYLYEARRPYFYPELLYKECCADKCLPKSARCAKFGERAKAWARLSQFPNAFKVTDLKNECCHGDLLECADDRLKYNDSKLCCKPLEKHCIEEDPDLDFEKVCKYEAKDFLGFLYERRHPVLKYELECCADCYVFDLEPNLKCLYFQALRYTKPQPTLSLKGCCER +>TestSequence3 +ERNCFHDDPPCDFKYLYEARRPYFYPELLYNECCADKCLPKSARCAKFGERAKAWARLSQFPKAFKVTDLKHECCHGDLLECADDRLKYNDSKLCCKPLEKHCIEEDPNLDFEKVCKYEAKDFLGFLYERRHPVLKYELECCADCYVFDLEPNLKCLYFQALRYTKPQPTLSLKGCCER +>TestSequence4 +ERNCFHDDPPCNFKYLYEARRPYFYPELLYKECCADKCLPKSARCAKFGERAKAWARLSQFPKAFKVTDLKHECCHGDLLECADDRLKYNDSKLCCKPLEKHCIEEDPDLDFEKVCKYEAKDFLGFLYERRHPVLKYELECCADCYVFDLEPNLKCLYFQALRYTKPQPTLSLKGCCER |
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| diff -r 000000000000 -r ab2cf9c6c4f1 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Mar 15 06:07:50 2016 -0400 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="noisy" version="1.5.12"> + <repository changeset_revision="289d9da141b8" name="package_noisy_1_5_12" owner="dcorreia" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |