Mercurial > repos > dcorreia > noisy
changeset 2:52238a3c4773 draft default tip
Uploaded
| author | dcorreia |
|---|---|
| date | Thu, 27 Oct 2016 07:44:54 -0400 |
| parents | 3b7dde5c3ec4 |
| children | |
| files | noisy.xml |
| diffstat | 1 files changed, 8 insertions(+), 30 deletions(-) [+] |
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--- a/noisy.xml Wed Mar 23 06:49:51 2016 -0400 +++ b/noisy.xml Thu Oct 27 07:44:54 2016 -0400 @@ -5,21 +5,8 @@ </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 - + + --seqtype $seqtype --cutoff $cutoff --distance $distance #if $usematrix.matrix == "true": @@ -48,20 +35,11 @@ </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="cfg"> - <param name="input_info" type="data" format="txt" label="info" help="Precompute file containning sequence description (dna or protein)" /> - </when> - </conditional> + <param name="seqtype" type="select" label="Sequence Coding"> + <option value="D">DNA</option> + <option value="P">Protein</option> + <option value="R">RNA</option> + </param> <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> @@ -91,7 +69,7 @@ </param> <when value="nnet"/> <when value="qnet"/> - <option value="all"/> + <when value="all"/> <when value="rand"> <param name="randpermut" type="integer" value="1000" label="random permutation"/> </when>