Mercurial > repos > edward-kirton > muscle
changeset 0:38a28f5f9449 default tip
Uploaded
author | edward-kirton |
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date | Thu, 14 Jul 2011 22:10:56 -0400 |
parents | |
children | |
files | muscle.xml |
diffstat | 1 files changed, 102 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/muscle.xml Thu Jul 14 22:10:56 2011 -0400 @@ -0,0 +1,102 @@ +<tool id="muscle" name="Muscle" version="1.0.0"> +<description>Multiple sequence alignment</description> +<command>muscle +-quiet +#if $input.select == '1': +-in $input.file +#else: +-profile +-in1 $input.file1 +-in2 $input.file2 +#end if +#if $usetree.select == 'yes': +-usetree_nowarn $usetree.file +#end if +$refine +-out $output +$diags +-maxiters $maxiters +-maxhours $maxhours +#if $advanced.select == 'yes': +-maxtrees $advanced.maxtrees +-anchorspacing $advanced.anchorspacing +-diagbreak $advanced.diagbreak +-diaglength $advanced.diaglength +-diagmargin $advanced.diagmargin +-smoothwindow $advanced.smoothwindow +$advanced.brenner +$advanced.dimer +#end if +</command> +<inputs> +<conditional name="input"> + <param name="select" type="select" label="Mode"> + <option value="1" selected="true">Single file</option> + <option value="2">Profile-profile alignment</option> + </param> + <when value="1"> + <param name="file" type="data" format="fasta" label="Unaligned sequences" /> + </when> + <when value="2"> + <param name="file1" type="data" format="fasta" label="Aligned sequences #1" /> + <param name="file2" type="data" format="fasta" label="Aligned sequences #2" /> + </when> +</conditional> +<conditional name="usetree"> + <param name="select" type="select" label="Use guide tree" help="NB: The best guide tree for multiple alignment is not in general the correct evolutionary tree"> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + <param name="file" type="hidden" value="" /> + </when> + <when value="yes"> + <param name="file" type="data" format="phylip" label="Guide tree in Newick/Phylip format" /> + </when> +</conditional> +<param name="refine" type="boolean" truevalue="-refine" falsevalue="" label="Refine an existing alignment" /> +<param name="diags" type="boolean" truevalue="-diags" falsevalue="" label="Find diagonals" help="Faster for similar sequences" /> +<param name="maxiters" label="Maximum number of iterations" type="integer" value="16" help="Use small number for very large files (as low as 1 or 2)." /> +<param name="maxhours" label="Maximum hours" type="float" value="24.0" help="If this time is exceeded, muscle will write out current alignment and stop." /> +<conditional name="advanced"> + <param name="select" type="select" label="Show advanced options"> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <param name="maxtrees" label="Maximum number of new trees to create in iteration 2" type="integer" value="1" /> + <param name="anchorspacing" label="Minimum spacing between anchor columns" type="integer" value="32" /> + <param name="diagbreak" label="Maximum distance between two diagonals that allows them to merge into one diagonal" type="integer" value="1" /> + <param name="diaglength" label="Minimum length of diagonal" type="integer" value="24" /> + <param name="diagmargin" label="Discard this many positions at ends of diagonal" type="integer" value="5" /> + <param name="smoothwindow" label="Window used for anchor column smoothing" type="integer" value="7" /> + <!-- flags --> + <param name="brenner" label="Use Steven Brenner's method for computing the root alignment" type="boolean" truevalue="-brenner" falsevalue="" selected="false" /> + <param name="dimer" label="Use dimer approximation for the SP score" help="Faster, slightly less accurate" type="boolean" truevalue="-dimer" falsevalue="" selected="false" /> + </when> +</conditional> +</inputs> +<outputs> +<data format="fasta" name="output" /> +</outputs> +<help> +**What it does** + +Perform multiple sequence alignment. + +**Documentation** + +http://www.drive5.com/muscle/muscle_userguide3.8.pdf + +**Author** + +Robert C. Edgar + +**Citation** + +Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. + +</help> +</tool>