Mercurial > repos > boris > phylorelatives
changeset 38:c340422b78b1 draft
Edited xml tool description
| author | boris |
|---|---|
| date | Tue, 25 Jun 2013 00:41:27 -0400 |
| parents | 0f66636a3f88 |
| children | 369f0b641498 |
| files | phylorelatives.xml |
| diffstat | 1 files changed, 23 insertions(+), 16 deletions(-) [+] |
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--- a/phylorelatives.xml Fri Jun 14 13:38:45 2013 -0400 +++ b/phylorelatives.xml Tue Jun 25 00:41:27 2013 -0400 @@ -40,12 +40,12 @@ </conditional> <param name="pairwise" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Use pairwise deletion of gaps/missing data" help="Defaults to "Complete deletion""/> <param name="iterations" type="integer" value="1000" label="Change number of bootstrap replicas" help="0 to deactivate"/> - <param name="major_only" type="boolean" truevalue="-j" falsevalue="" checked="False" label="Major-alleles-only mode" help="Useful to generate background tree"/> + <param name="major_only" type="boolean" truevalue="-j" falsevalue="" checked="False" label="Major-alleles-only mode" help="All sequences will be treated as major allele sequences. Useful to generate background tree"/> </inputs> <outputs> <data format="fasta" name="multifasta" label="${tool.name} on ${on_string}: multifasta used" /> <data format="tabular" name="siblings" label="${tool.name} on ${on_string}: relatives list"/> - <data format="txt" name="newick" label="${tool.name} on ${on_string}: newick"/> + <data format="txt" name="newick" label="${tool.name} on ${on_string}: newick string"/> <data format="png" name="plot" label="${tool.name} on ${on_string}: tree plot"/> </outputs> <tests> @@ -60,8 +60,8 @@ -Major allele and its closely related minor allele sequence are expected to cluster together in a tree. -Deviation from expectation allows to trace back potential contamination from unrelated samples. +The major and minor allele sequences of a sample are expected to cluster together in a phylogenetic tree. +Deviation from expectation suggests potential contamination coming from the closest unrelated samples. ----- @@ -71,7 +71,7 @@ Constructs relatedness of a set of sequences based on the pairwise proportion of different sites. One or more test sequences are accepted as long as their name include the strict suffix "_minor" or "_test" (i.e. >seq1_minor). -It returns the FASTA multiple alignment used, and reports a table with the closest major allele relatives per minor allele sequence, the tree plot and newick string of the tree. +It returns the FASTA multiple alignment used, and reports a table with the closest major allele relatives, the tree plot and newick string of the tree. ----- @@ -80,7 +80,7 @@ **Note** This tools DOES NOT align the sequences. -Consequently, same length homologous sequences are required as input to fabricate a FASTA multiple alignment by concatenation if more than one FASTA file is provided. +Consequently, same length homologous sequences are required as input to fabricate a FASTA multiple alignment by concatenation of individual FASTA files. ----- @@ -92,22 +92,29 @@ See http://www.bioperl.org/wiki/FASTA_multiple_alignment_format +*Newick* + +http://www.megasoftware.net/WebHelp/glossary/rh_newick_format.htm + ----- **Example** -- For the following dataset:: - >sample1_major - >sample1_minor - >sample2_major - >sample3_major - >sample4_major +- For the multiple alignment composed of the following FASTA files:: + + >sample1_major + >sample1_minor + >sample2_major + >sample3_major + >sample4_major -- running this tool with *b = 1000* *m = yes* *root = RSRS*, will return:: - newick - relatives - plot +- running this tool with *root = RSRS.fasta*, and default parameters will return four datasets:: + + 1. multiple alignment file used for running the tool + 2. relatives of sample1_minor + 3. NJ tree newick string (rooted on RSRS) + 4. NJ tree png plot (rooted on RSRS) -----