| Previous changeset 4:f97743d52b87 (2020-04-03) Next changeset 6:224c75ad0518 (2021-08-12) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559" |
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modified:
iqtree.xml iqtree_macros.xml |
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| diff -r f97743d52b87 -r fc06db7794f1 iqtree.xml --- a/iqtree.xml Fri Apr 03 09:04:30 2020 -0400 +++ b/iqtree.xml Wed Aug 11 13:42:01 2021 +0000 |
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| b'@@ -1,18 +1,19 @@\n-<tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@.3" >\n+<tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@+@VERSION_SUFFIX@" >\n <description>Phylogenomic / evolutionary tree construction from multiple sequences</description>\n <macros>\n+ <token name="@VERSION_SUFFIX@">galaxy0</token>\n <import>iqtree_macros.xml</import>\n </macros>\n <expand macro="requirements" />\n <command detect_errors="exit_code"><![CDATA[\n iqtree\n- -pre PREF\n+ --prefix PREF\n #if $general_options.short_alignments:\n- -nt 1\n+ -T 1\n #else:\n- -nt \\${GALAXY_SLOTS:-10}\n+ -T \\${GALAXY_SLOTS:-10}\n #end if\n- -redo\n+ --redo\n \n ## file\n #if $general_options.s\n@@ -22,171 +23,240 @@\n ## file\n #if $general_options.t\n -t \'$general_options.t\'\n- $tree_parameters.constructing_consensus.con\n- $tree_parameters.constructing_consensus.net\n- #if str($tree_parameters.constructing_consensus.bi) != \'\'\n- -bi \'$tree_parameters.constructing_consensus.bi\'\n+ $tree_parameters.constructing_consensus.con_tree\n+ $tree_parameters.constructing_consensus.con_net\n+ #if str($tree_parameters.constructing_consensus.burnin) != \'\'\n+ --burnin \'$tree_parameters.constructing_consensus.burnin\'\n #end if\n \n ## file\n- #if $tree_parameters.constructing_consensus.sup\n- -sup \'$tree_parameters.constructing_consensus.sup\'\n+ #if $tree_parameters.constructing_consensus.support\n+ --support \'$tree_parameters.constructing_consensus.support\'\n #end if\n \n #if str($tree_parameters.constructing_consensus.suptag) != \'\'\n- -suptag \'$tree_parameters.constructing_consensus.suptag\'\n+ --suptag \'$tree_parameters.constructing_consensus.suptag\'\n #end if\n \n ## file\n #if $tree_parameters.computing_robinson_foulds.rf\n -rf \'$tree_parameters.computing_robinson_foulds.rf\'\n- $tree_parameters.computing_robinson_foulds.rf_all\n+ $tree_parameters.computing_robinson_foulds.tree_dist_all\n $tree_parameters.computing_robinson_foulds.rf_adj\n #end if\n+ $tree_parameters.ancestral_state.ancestral\n+ #if $tree_parameters.ancestral_state.asr_min:\n+ --asr-min $tree_parameters.ancestral_state.asr_min\n+ #end if\n+ #if $tree_parameters.concordance_factor.gcf:\n+ --gcf \'$tree_parameters.concordance_factor.gcf\'\n+ #end if\n+ #if $tree_parameters.concordance_factor.scf:\n+ --scf \'$tree_parameters.concordance_factor.scf\'\n+ #end if\n+ $tree_parameters.concordance_factor.df_tree\n+ $tree_parameters.concordance_factor.cf_verbose\n+ $tree_parameters.concordance_factor.cf_quartet\n+ $tree_parameters.symmetry_test.symtest\n+ $tree_parameters.symmetry_test.symtest_remove_bad\n+ $tree_parameters.symmetry_test.symtest_remove_good\n+ $tree_parameters.symmetry_test.symtest_keep_zero\n+ #if $tree_parameters.symmetry_test.symtest_pval:\n+ --symtest-pval $tree_parameters.symmetry_test.symtest_pval\n+ #end if\n+ #if $tree_parameters.symmetry_test.symtest_type:\n+ --symtest-type $tree_parameters.symmetry_test.symtest_type\n+ #end if\n+#end if\n+\n+## date options\n+#if str($time_tree.date_source.select_source) == \'dataset\':\n+ #if $time_tree.date_source.date:\n+ --date $time_tree.date_source.date\n+ #end if\n+#elif str($time_tree.date_source.select_source) == \'input\':\n+ --date TAXNAME\n+ #if str($time_tree.date_source.date_tip) != \'\':\n+ --date-tip \'$time_tree.date_source.date_tip\'\n+ #end if\n+ #if str($time_tree.date_source.date_root) != \'\':\n+ --date-root \'$time_tree.date_source.date_root\'\n+ #end if\n+ #if str($time_tree.date_source.date_ci) != \'\':\n+ --date-ci \'$time_tree.date_source.date_ci\'\n+ #end if\n+ #if str($time_tree.date_source.clock_sd) != \'\':\n+ --clock-sd \'$time_tree.date_source.clock_sd\'\n+ #end if\n+ #if str($time_tree.date_source.date_outlier) != \'\':\n+ --date-outlier \'$time_tree.date_sou'..b'531.+MT019532.+" />\n+ </assert_contents>\n+ </output>\n </test>\n </tests>\n <help><![CDATA[\n@@ -721,7 +879,7 @@\n You can now start to reconstruct a maximum-likelihood tree\n from this alignment by entering (assuming that you are now in the same folder with `example.phy`):\n \n-::iqtree -s example.phy -st AA -seed 9999 -m TESTNEW -msub nuclear -madd LG4M,LG4x -merit AICc -bb 2000\n+::iqtree -s example.phy -st AA -seed 9999 -m TESTNEW -msub nuclear -madd LG4M,LG4x -merit AICc --ufboot 2000\n \n * **-s** is the option to specify the name of the alignment file\n \n@@ -737,7 +895,7 @@\n \n * **-merit** asserts the type of optimality criterion\n \n-* **-bb** defines the number of replicates\n+* **-ufboot** defines the number of replicates\n \n \n Each of these parameters are available under the relevant sub-sections in the main tool interface.\n@@ -835,9 +993,9 @@\n \n ::\n \n- iqtree -s example.phy -m TIM2+I+G -bb 1000\n+ iqtree -s example.phy -m TIM2+I+G --ufboot 1000\n \n-**-bb** specifies the number of bootstrap replicates where 1000 is the minimum number recommended. The section **MAXIMUM LIKELIHOOD TREE** in **example.phy.iqtree** shows a textual representation of the maximum likelihood tree with branch support values in percentage. The NEWICK format of the tree is printed to the file **example.phy.treefile**. In addition, IQ-TREE writes the following files:\n+**-ufboot** specifies the number of bootstrap replicates where 1000 is the minimum number recommended. The section **MAXIMUM LIKELIHOOD TREE** in **example.phy.iqtree** shows a textual representation of the maximum likelihood tree with branch support values in percentage. The NEWICK format of the tree is printed to the file **example.phy.treefile**. In addition, IQ-TREE writes the following files:\n \n * **example.phy.contree**: the consensus tree with assigned branch supports where branch lengths are optimized on the original alignment.\n \n@@ -855,7 +1013,7 @@\n \n Thus, if severe model violations are present in the data set at hand, users are advised to append **-bnni** to the regular UFBoot command:\n \n-iqtree -s example.phy -m TIM2+I+G -bb 1000 -bnni\n+iqtree -s example.phy -m TIM2+I+G --ufboot 1000 -bnni\n \n For more details see:\n \n@@ -881,9 +1039,9 @@\n \n ::\n \n- iqtree -s example.phy -m TIM2+I+G -alrt 1000\n+ iqtree -s example.phy -m TIM2+I+G --alrt 1000\n \n-**-alrt** specifies the number of bootstrap replicates for SH-aLRT where 1000 is the minimum number recommended.\n+**--alrt** specifies the number of bootstrap replicates for SH-aLRT where 1000 is the minimum number recommended.\n \n IQ-TREE also supports other tests such as the aBayes test (Anisimova et al., 2011) and the local bootstrap test (Adachi and Hasegawa, 1996).\n \n@@ -891,7 +1049,7 @@\n \n ::\n \n- iqtree -s example.phy -m TIM2+I+G -alrt 1000 -bb 1000\n+ iqtree -s example.phy -m TIM2+I+G --alrt 1000 --ufboot 1000\n \n The branches of the resulting **.treefile** will be assigned with both SH-aLRT and UFBoot support values, which are readable by any tree viewer program like FigTree, Dendroscope or ETE. You can also look at the textual tree figure in **.iqtree** file:\n \n@@ -938,7 +1096,12 @@\n From this figure, the branching patterns within reptiles are poorly supported (e.g. **Sphenodon** with SH-aLRT: 39%, UFBoot: 51% and **Turtle** with SH-aLRT: 85%, UFBoot: 72%) as well as the phylogenetic position of **Seal** within mammals (SH-aLRT: 68.3%, UFBoot: 75%). Other branches appear to be well supported.\n ]]></help>\n <citations>\n+ <citation type="doi">10.1038/nmeth.4285</citation>\n <citation type="doi">10.1093/molbev/msu300</citation>\n+ <citation type="doi">10.1093/molbev/msx281</citation>\n+ <citation type="doi">10.1093/sysbio/syx068</citation>\n+ <citation type="doi">10.1093/sysbio/syw037</citation>\n+ <citation type="doi">10.1016/j.jtbi.2016.07.042</citation>\n <citation type="doi">10.1093/molbev/mst024</citation>\n </citations>\n </tool>\n' |
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| diff -r f97743d52b87 -r fc06db7794f1 iqtree_macros.xml --- a/iqtree_macros.xml Fri Apr 03 09:04:30 2020 -0400 +++ b/iqtree_macros.xml Wed Aug 11 13:42:01 2021 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.5.5</token> + <token name="@TOOL_VERSION@">2.1.2</token> <xml name="requirements"> <requirements> |