annotate phylogenies/phytab_raxml_pars.xml @ 0:5b9a38ec4a39 draft default tip

First commit of old repositories

<tool id="phytab_raxml_pars" name="Phytab RAxML-Parsimony" version="1.0">
  <description>Phytab RAxML - Parsimony for phytab format</description>
  <requirements>
    <requirement type="package">raxml</requirement>
  </requirements>
  <command interpreter="python">
    phytab_raxml_pars.py -i $sequence -e $evo -f $efile -T 4> $stdout 2>&amp;1
  </command>
<!-- if using a queuing system, make sure number of ppn in jobrunner matches threads as set above -->

  <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">DNA</option> <option value="PROTGAMMADAYHOFF">PROTEIN</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 ${on_string}: stdout" />
    <data format="tabular" name="Parsimony Tree(s)" label="${tool.name} on ${on_string}: results" from_work_dir="results/parsimony_results.txt" />
  </outputs>
  <tests>
  </tests>
  <help>
**What it does**
This tool computes a randomized parsimony starting tree with RAxML (-y argument).  Single or multi-gene phytab files accepted.

Also, see RAxML site for additional information: https://github.com/stamatak/standard-RAxML

**Output**
A tab-delimited file containing partition-name and newick parsimony tree on each line.  This output is accepted by the tool 'RAxML using Starting Trees' to optimize branch lengths for each 
partition. 

Please direct questions or comments to [e-mail] or, if you can, enter them on the osiris_phylogenetics site at bitbucket.org

-------    

**Citations**   

This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider citing the following.

Current Osiris Citation is here

http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
 
 </help>
</tool>