Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
diff phylostatistics/phytab_LB_pruner.xml @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phylostatistics/phytab_LB_pruner.xml Tue Mar 11 12:19:13 2014 -0700 @@ -0,0 +1,59 @@ +<tool id="phytab_LB_pruner" name="Phytab_LB_Pruner" version="1.0"> + <description>LB_pruner: Identify genes on very long branches.</description> + <requirements> + <requirement type="package">LB_prunerG.pl</requirement> + </requirements> + <command interpreter="python"> + phytab_LB_pruner.py -i $data -m $multiplier + </command> + <inputs> + <param format="txt" name="data" type="data" label="Sequence data" help="This should be sequence data in phytab or FASTA"/> + <param name="multiplier" type="float" value="4" label="Multiplier" help="Value of Multiplier, M. Branches longer than M times average are written to +file" > + </param> + </inputs> + <outputs> + <data format="tabular" name="LB pruner results" label="${tool.name} on ${on_string}: results" from_work_dir="data/results.data" /> + </outputs> + <tests> + </tests> + <help> +**What it does** + +LB pruner will find the average of all branch lengths in each Newick tree. Given the user-input multiplier value (M), if any branch is longer than Mx +the average branch length, that gene will be written to the tab-delimited output file. See outputs section for more information. + +------ + +**Inputs** + +Sequence data file in phytab or FASTA. + +Phytab description: http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html + +Input a table as follows::: + name newick_tree; + name2 newick_tree; + name3 newick_tree; + +Enter a value for M, the multiplier. + +------ + +**Outputs** + +Tab delimited file listing any genes longer than Mx the average branch length for each Newick tree. If an internal branch is longer than M times the +average then all members of that clade are written to the out file, with 999 as the length of each branch. The third column is branch length, fourth +column is average branch length for each tree. + +------- + +**Citations** + +This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider citing the following. + +Current Osiris Citation is here + +http://osiris-phylogenetics.blogspot.com/2012/10/citation.html + </help> +</tool>