Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

view phylogenies/phytab_raxml_small.xml @ 0:5b9a38ec4a39 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
parents
children
line wrap: on
line source

<tool id="phytab_raxml_small" name="Phytab RAxML SMALL" version="1.0">
  <description>Phytab RAxML SMALL - RAxML for phytab format. Calls only 1 node for 3 hours</description>
  <requirements>
    <requirement type="package">raxml</requirement>
  </requirements>
  <command interpreter="python">
    phytab_raxml.py -i $sequence -e $evo -f $efile -T 4> $stdout 2>&amp;1
  </command>
  <inputs>
    <param format="tabular" name="sequence" type="data" label="PHYTAB sequence file"/>
    <param name="evo" type="select" format="text">
      <label>Model of evolution to apply to all data partitions (-m)</label>
      <option value="GTRGAMMA">GTRGAMMA</option> <option value="PROTGAMMADAYHOFF">PROTGAMMADAYHOFF</option> <option value="PROTGAMMADCMUT">PROTGAMMADCMUT</option> <option value="PROTGAMMAJTT">PROTGAMMAJTT</option> <option value="PROTGAMMAMTREV">PROTGAMMAMTREV</option> <option value="PROTGAMMAWAG">PROTGAMMAWAG</option> <option value="PROTGAMMARTREV">PROTGAMMARTREV</option> <option value="PROTGAMMACPREV">PROTGAMMACPREV</option> <option value="PROTGAMMAVT">PROTGAMMAVT</option> <option value="PROTGAMMABLOSUM62">PROTGAMMABLOSUM62</option> <option value="PROTGAMMAMTMAM">PROTGAMMAMTMAM</option> <option value="PROTGAMMALG">PROTGAMMALG</option> <option value="PROTGAMMAMTART">PROTGAMMAMTART</option> <option value="PROTGAMMAMTZOA">PROTGAMMAMTZOA</option> <option value="PROTGAMMAPMB">PROTGAMMAPMB</option> <option value="PROTGAMMAHIVB">PROTGAMMAHIVB</option> <option value="PROTGAMMAHIVW">PROTGAMMAHIVW</option> <option value="PROTGAMMAJTTDCMUT">PROTGAMMAJTTDCMUT</option> <option value="PROTGAMMAFLU">PROTGAMMAFLU</option> <option value="PROTGAMMAGTR">PROTGAMMAGTR</option>
    </param>
    <param format="txt" name="efile" type="data" optional="true" value="n" label="Tab-delimited file with partition name in first column, evolutionary model in the second column. Must be RAxML 
valid model names. (optional)"/>
  </inputs>
  <outputs>
    <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout" />
    <data format="tabular" name="results.phy" label="${tool.name} on ${on_string}: results" from_work_dir="results/results.phy" />
  </outputs>
  <tests>
  </tests>
  <help>
  **Parallel RaXML**
See phytab description here: http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
  </help>
</tool>