Mercurial > repos > dcorreia > noisy
changeset 0:cd681b5409d4 draft
Uploaded
| author | dcorreia |
|---|---|
| date | Mon, 01 Feb 2016 09:34:31 -0500 |
| parents | |
| children | 5eaa851e6b44 |
| files | noisy.xml |
| diffstat | 1 files changed, 160 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/noisy.xml Mon Feb 01 09:34:31 2016 -0500 @@ -0,0 +1,160 @@ +<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 == 'auto' : + ## 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="auto">Read this information in a 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">Provide 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 avarage over INT columns" /> + <param name="shuffles" type="integer" value="0" min="0" label="Perform INT random shuffles per column" /> + </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" /> + </outputs> +<help> +<![CDATA[ +Usage:: + + noisy [OPTIONS] MultiFastaAlignment + +Options:: + + --cutoff FLOAT Set cutoff value to FLOAT. + (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 + rand[,INT] sample INT random permutation + (default is >1000<) + INT,INT,... provide ordering explicitly as + comma-seperated string of INTs + all all permutations + + --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>