| Next changeset 1:ac4a2f2b998b (2016-05-08) |
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Commit message:
Uploaded |
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added:
phyml.xml |
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| diff -r 000000000000 -r a09846dcba83 phyml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyml.xml Sat May 07 10:51:55 2016 -0400 |
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| @@ -0,0 +1,127 @@ +<tool id="phyml" name="PhyML" version="0.1.0"> + <description> Phylogeny software based on the maximum-likelihood principle </description> + <requirements> + <package name="phyml" version="3.1"/> + </requirements> + <command><![CDATA[ + ln -sf $input input_phy; + + phyml -i input_phy + $format + + -n $nb_data_set + -d $type.type_of_seq + + #if ($type.type_of_seq == "nt"): + -t $type.tstv + #end if + + -m $type.model + + #if (str($bs.bootstrap) in ['0','-1','-2','-4']): + -b $bs.bootstrap + #elif (str($bs.bootstrap) == '1'): + -b $bs.bootstrap.replicate_num + #end if + + -f $character_freq + -v $prop_invar + -c $nb_subst_cat + -a $gamma + -s $search_move + -o $optimisation_parameter + + > ${stdout_output}; + ]]> + </command> + <inputs> + <param name="input" format="txt" type="data" label="Source file" help="Select the input file"/> + <param name="format" type="select" label="Choose between interleaved format or sequential format" display="radio"> + <option value="">Interleaved</option> + <option value="--sequential">Sequential</option> + </param> + <param name="nb_data_set" type="integer" value="1" label="Number of data sets"/> + + <conditional name="type"> + <param name="type_of_seq" type="select" label="Data type" help="Select between nucleic acids or amino acids" display="radio"> + <option value="nt">Nucleic acids</option> + <option value="aa">Amino acids</option> + </param> + <when value="nt"> + <param name="tstv" type="text" value="e" label="Transition/transversion ratio" help="Can be a fixed positive value or type 'e' to get the maximum likelihood estimate"/> + <param name="model" type="select" label="Nucleotide-based models" display="radio"> + <option value="HKY85">HKY85</option> + <option value="JC69">JC69</option> + <option value="K80">K80</option> + <option value="F81">F81</option> + <option value="F84">F84</option> + <option value="TN93">TN93</option> + <option value="GTR">GTR</option> + </param> + </when> + + <when value="aa"> + <param name="model" type="select" label="Amino-acid based models" display="radio"> + <option value="LG">LG</option> + <option value="WAG">WAG</option> + <option value="JTT">JTT</option> + <option value="MtREV">MtREV</option> + <option value="Dayhoff">Dayhoff</option> + <option value="DCMut">DCMut</option> + <option value="RtREV">RtREV</option> + <option value="CpREV">CpREV</option> + <option value="VT">VT</option> + <option value="Blosum62">Blosum62</option> + <option value="MtMam">MtMam</option> + <option value="MtArt">MtArt</option> + <option value="HIVw">HIVw</option> + <option value="HIVb">HIVb</option> + </param> + </when> + </conditional> + + <conditional name="bs"> + <param name="bootstrap" type="select" min="1" value="100" label="Branch supports" display="radio"> + <option value="0">No bootstrap</option> + <option value="1">Number of bootstrap</option> + <option value="-1">Likelihood ratio test using aLRT statistics</option> + <option value="-2">Likelihood ratio test using Chi2</option> + <option value="-4" selected='true'>SH-like</option> + </param> + <when value="1"> + <param name="replicate_num" type="integer" min="1" value="100" label="Number of bootstrap replicates"/> + </when> + </conditional> + + <param name="character_freq" type="select" label="Character frequencies" display="radio"> + <option value="e">Empirical</option> + <option value="m">ML/Model</option> + </param> + <param name="prop_invar" type="text" value="e" label="Proportion of invariable sites" help="Can be a fixed value in the [0,1] range or type 'e' to get the maximum likelihood estimate"/> + <param name="nb_subst_cat" type="integer" min="1" value="4" label="Number of relative substitution rate categories" help="Must be a positive integer"/> + <param name="gamma" type="text" value="e" label="Value of the gamma shape parameter" help="Can be a fixed positive value or 'e' to get the maximum likelihood estimate"/> + <param name="search_move" type="select" label="Tree topology search operation option" display="radio"> + <option value="NNI">NNI</option> + <option value="SPR">SPR</option> + <option value="BEST">Best of NNI and SPR search</option> + </param> + <param name="optimisation_parameter" type="select" label="Optimise topology" display="radio"> + <option value="tlr">Tree topology, branch length and substitution rate parameters</option> + <option value="tl">Tree topology and branch lengths</option> + <option value="lr">Branch lengths and substitution rate parameters</option> + <option value="l">Branch lengths</option> + <option value="r">Substitution rate parameters</option> + <option value="n">No parameter is optimized</option> + </param> + </inputs> + + <outputs> + <data name="output_tree" format="txt" label="Output_tree" from_work_dir="*_phyml_tree.txt"/> + <data name="output_stats" format="txt" label="Output_stats" from_work_dir="*_phyml_stats.txt"/> + <data name="stdout_output" label="Output_stdout" format="txt"/> + </outputs> + +</tool> + + + |