Mercurial > repos > iuc > hyphy_absrel
diff hyphy_absrel.xml @ 9:cce7b18495e4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
author | iuc |
---|---|
date | Fri, 27 Mar 2020 13:14:17 -0400 |
parents | f73435dc282b |
children | 4cc4dbca2f02 |
line wrap: on
line diff
--- a/hyphy_absrel.xml Thu Mar 19 10:14:27 2020 -0400 +++ b/hyphy_absrel.xml Fri Mar 27 13:14:17 2020 -0400 @@ -17,6 +17,8 @@ #if $log: > '$absrel_log' #end if + ; + @CATCH_MPIERR@ ]]></command> <inputs> <expand macro="inputs"/> @@ -39,10 +41,10 @@ </test> </tests> <help><![CDATA[ - + aBSREL : Adaptive Branch-Site Random Effects Likelihood -======================================================= - +======================================================= + What question does this method answer? -------------------------------------- @@ -52,7 +54,7 @@ ------------------------ 1. Exploratory testing for evidence of lineage-specific positive diversifying selection in small to medium sized alignments (up to 100 sequences). -2. Targeted testing of branches selected a priori for positive diversifying selection, including alignments with prohibitive runtimes under older branch-site models (up to 1,000 sequences) +2. Targeted testing of branches selected a priori for positive diversifying selection, including alignments with prohibitive runtimes under older branch-site models (up to 1,000 sequences) Brief description ----------------- @@ -77,7 +79,7 @@ A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf). -For each tested branch the analysis will infer the appropriate number of selective regimes, +For each tested branch the analysis will infer the appropriate number of selective regimes, and whether or not there is statistical evidence of positive selection on that branch. A custom visualization module for viewing these results is available (see http://vision.hyphy.org/aBSREL for an example) @@ -93,22 +95,22 @@ :: - --code Which genetic code to use + --code Which genetic code to use --branches Which branches should be tested for selection? All [default] : test all branches - - Internal : test only internal branches (suitable for + + Internal : test only internal branches (suitable for intra-host pathogen evolution for example, where terminal branches may contain polymorphism data) - + Leaves: test only terminal (leaf) branches - + Unlabeled: if the Newick string is labeled using the {} notation, - test only branches without explicit labels + test only branches without explicit labels (see http://hyphy.org/tutorials/phylotree/) - + ]]></help> <expand macro="citations">