Mercurial > repos > dereeper > phyml
changeset 12:7f2fdaeaa723 draft
Uploaded
author | dcorreia |
---|---|
date | Tue, 25 Oct 2016 12:48:04 -0400 |
parents | b0d5f7b87402 |
children | bb8875d6dc35 |
files | phyml.xml |
diffstat | 1 files changed, 9 insertions(+), 7 deletions(-) [+] |
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--- a/phyml.xml Wed Oct 19 13:16:07 2016 -0400 +++ b/phyml.xml Tue Oct 25 12:48:04 2016 -0400 @@ -11,11 +11,14 @@ source="stdrr" level="fatal"/> </stdio> - - <command><![CDATA[ + <command> + <![CDATA[ ##PhyML outputs are based on input path and we need to create outputs in working_dir. ln -sf $input '${input.name}'; - + #if ($usetree.inputTree == "true"): + ln -sf ${$usetree.userInputTree} ${$usetree.userInputTree.name}; + #end if + phyml --input '${input.name}' ${phylip_format} --datatype ${seq.type_of_seq} @@ -45,17 +48,16 @@ -o ${optimisationTopology} #if ($usetree.inputTree == "true"): - --inputtree ${inputTree.userInputTree} + --inputtree ${$usetree.userInputTree.name} #end if #if ($numStartSeed != "0"): --r_seed ${numStartSeed} #end if - --no_memory_check - --quiet > ${output_stdout}; + --no_memory_check > ${output_stdout}; grep 'failed' ${output_stdout} >&2; - ]]> + ]]> </command> <inputs> <param name="input" type="data" format="phylip, phy" label="Alignment file" help="phylip format"/>