Mercurial > repos > boris > phylorelatives
changeset 41:9453ba52f46b draft
tool now uses multiple selection for input fasta files
| author | boris |
|---|---|
| date | Fri, 19 Jul 2013 17:46:03 -0400 |
| parents | dd39849c2ff1 |
| children | 35741a74d073 |
| files | phylorelatives.xml |
| diffstat | 1 files changed, 7 insertions(+), 10 deletions(-) [+] |
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--- a/phylorelatives.xml Fri Jul 19 17:44:58 2013 -0400 +++ b/phylorelatives.xml Fri Jul 19 17:46:03 2013 -0400 @@ -7,34 +7,31 @@ <requirement type="package" version="3.0-8">ape</requirement> </requirements> <command interpreter="python">phylorelatives.py - #for $sequence in $sequences: - -i "${sequence.sequence}" + #for $sequence in ( $sequences ): + -i "${sequence}" #end for -m "${multifasta}" -b "$iterations" $pairwise $major_only - #if str($root.root_selector)=="upload_root": + #if str($root.root_selector)=="add_root": -r "${root.root_fa}" #end if --relatives-out "$siblings" --newick-out "$newick" --trees-out "$plot" - </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="Minor allele sequences must be labeled "_minor" or "_test" e.g. ">sample1_minor""> + <param format="fasta" name="sequences" type="data" label="FASTA file" multiple="TRUE" help="Minor allele sequences must be labeled "_minor" or "_test" e.g. ">sample1_minor""> </param> - </repeat> <conditional name="root"> <param name="root_selector" type="select" label=" Root sequence"> <option value="unrooted" selected="True"></option> - <option value="upload_root"></option> + <option value="add_root"></option> </param> <when value="unrooted"> </when> - <when value="upload_root"> + <when value="add_root"> <param name="root_fa" format="fasta" type="data" label="Root tree using" help="Must have the same length as input sequences"/> </when> </conditional> @@ -51,7 +48,7 @@ <tests> <test> <param name="iterations" value="0"/> - <param name="sequence" value="test.fa"/> + <param name="sequences" value="test.fa"/> <output name="siblings" file="test.fa-siblings.tab"/> </test> </tests>