| Previous changeset 5:fc06db7794f1 (2021-08-11) Next changeset 7:524d31add34a (2021-08-13) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01" |
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modified:
iqtree.xml |
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| diff -r fc06db7794f1 -r 224c75ad0518 iqtree.xml --- a/iqtree.xml Wed Aug 11 13:42:01 2021 +0000 +++ b/iqtree.xml Thu Aug 12 07:52:10 2021 +0000 |
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| @@ -294,9 +294,9 @@ -r '$tree_parameters.generating_random.r' #end if -$tree_parameters.generating_random.r -$tree_parameters.generating_random.rand - +#if $tree_parameters.generating_random.rand + $tree_parameters.generating_random.rand +#end if #if str($tree_parameters.generating_random.branch_min) != '' and str($tree_parameters.generating_random.branch_mean) != '' and str($tree_parameters.generating_random.branch_max) != '' --rlen $tree_parameters.generating_random.branch_min $tree_parameters.generating_random.branch_mean $tree_parameters.generating_random.branch_max @@ -426,6 +426,29 @@ </when> <when value="false"> <param argument="-m" type="select" label="Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein)" > + <help><![CDATA[ +<b>Note:</b> Only <code>TEST</code> and custom models that do not rely on <code>MF</code> can be used in conjunction with bootstrap parameters (-b)<br/><br/> +IQ-TREE also works for codon, binary and morphogical data. +<table> + <tr> + <td><i>TESTONLY</i></td> + <td>Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein). Moreover, IQ-TREE also works for codon, binary and morphogical data.</td> + </tr> + <tr> + <td><i>TEST</i></td> + <td>Like -m TESTONLY but immediately followed by tree reconstruction using the best-fit model found. So this performs both model selection and tree inference within a single run.</td> + </tr> + <tr> + <td><i>MF</i></td> + <td>Best-fit model selection without tree reconstruction.</td> + </tr> + <tr> + <td><i>MFP</i></td> + <td>Extended model selection with FreeRate heterogeneity immediately followed by tree inference.</td> + </tr> +</table> +]]> + </help> <option value="" selected="true">(None)</option> <option value="TESTONLY">Standard model selection</option> <option value="TEST">Standard model selection followed by tree inference</option> @@ -586,9 +609,11 @@ </section> <section name="generating_random" expanded="False" title="Generating random trees"> <param argument="-r" type="integer" optional="true" label="Specify number of taxa" help="IQ-TREE will create a random tree under Yule-Harding model with specified number of taxa"/> - <param argument="--rand" type="boolean" truevalue="--rand UNI" falsevalue="" checked="false" label="Like -r, but a random tree is created under uniform model."/> - <param argument="--rand" type="boolean" truevalue="--rand CAT" falsevalue="" checked="false" label="Like -r, but a random caterpillar tree is created."/> - <param argument="--rand" type="boolean" truevalue="--rand BAL" falsevalue="" checked="false" label="Like -r, but a random balanced tree is created."/> + <param argument="--rand" type="select" optional="true" label="Random tree creation"> + <option value="--rand UNI">Uniform model</option> + <option value="--rand CAT">Random caterpillar tree</option> + <option value="--rand BAL">Random balanced tree</option> + </param> <param name="branch_min" type="integer" optional="true" label="Minimum branch lengths of the random tree" /> <param name="branch_mean" type="integer" optional="true" label="Median branch lengths of the random tree" /> <param name="branch_max" type="integer" optional="true" label="Maximum branch lengths of the random tree" /> @@ -662,7 +687,7 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="6"> <param name="seed" value="1257" /> <param name="seqtype" value="AA" /> <param name="s" value="example.phy" /> @@ -707,7 +732,7 @@ </assert_contents> </output> </test> - <test> + <test expect_num_outputs="6"> <!-- bootstrap sans model --> <param name="seed" value="1257" /> <param name="seqtype" value="AA" /> @@ -741,7 +766,7 @@ </assert_contents> </output> </test> - <test> + <test expect_num_outputs="6"> <!-- model sans bootstrap --> <param name="seed" value="1257" /> <param name="seqtype" value="AA" /> @@ -775,7 +800,7 @@ </assert_contents> </output> </test> - <test> + <test expect_num_outputs="6"> <param name="s" value="example.phy" /> <output name="iqtree"> <assert_contents> @@ -788,7 +813,7 @@ </assert_contents> </output> </test> - <test> + <test expect_num_outputs="6"> <param name="s" value="example.phy" /> <param name="opt_custommodel" value="true" /> <param name="m" value="GTR+G{0.9}" /> @@ -803,7 +828,7 @@ </assert_contents> </output> </test> - <test> + <test expect_num_outputs="6"> <param name="s" value="short.fasta" /> <param name="short_alignments" value="true" /> <output name="treefile"> |