Mercurial > repos > boris > phylorelatives
changeset 34:6935429eef05 draft
Updfated xml with -j option
| author | boris |
|---|---|
| date | Fri, 14 Jun 2013 13:27:49 -0400 |
| parents | 8d663949bdc8 |
| children | 015d1fb47ec4 |
| files | phylorelatives.xml |
| diffstat | 1 files changed, 9 insertions(+), 4 deletions(-) [+] |
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--- a/phylorelatives.xml Mon Jun 10 00:48:11 2013 -0400 +++ b/phylorelatives.xml Fri Jun 14 13:27:49 2013 -0400 @@ -13,6 +13,7 @@ -m "${multifasta}" -b "$iterations" $pairwise + $major_only #if str($root.root_selector)=="upload_root": -r "${root.root_fa}" #end if @@ -23,7 +24,7 @@ </command> <inputs> <repeat name="sequences" title="Input FASTA file" min="1" help="Files will be concatenated into a single FASTA multiple alignment file, thus equal length homologous sequences are required"> - <param format="fasta" name="sequence" type="data" label="FASTA file" help="Requires at least one minor allele sequence properly labeled "_minor" or "_test" e.g. ">sample1_minor""> + <param format="fasta" name="sequence" type="data" label="FASTA file" help="Minor allele sequences must be labeled "_minor" or "_test" e.g. ">sample1_minor""> </param> </repeat> <conditional name="root"> @@ -38,11 +39,12 @@ </when> </conditional> <param name="pairwise" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Use pairwise deletion of gaps/missing data" help="Defaults to "Complete deletion""/> - <param name="iterations" type="integer" value="1000" label="Change number of bootstrap replicas" help="0 to deactivate"/> + <param name="iterations" type="integer" value="1000" label="Change number of bootstrap replicas" help="0 to deactivate"/> + <param name="major_only" type="boolean" truevalue="-j" falsevalue="" checked="False" label="Major-alleles-only mode" help="Useful to generate background tree"/> </inputs> <outputs> - <data format="fasta" name="multifasta" label="${tool.name} on ${on_string}: multifasta" /> - <data format="tabular" name="siblings" label="${tool.name} on ${on_string}: relatives"/> + <data format="fasta" name="multifasta" label="${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 ${on_string}: newick"/> <data format="txt" name="plot" label="${tool.name} on ${on_string}: ascii plot"/> </outputs> @@ -58,6 +60,9 @@ +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. + ----- .. class:: infomark