comparison pplacer.xml @ 6:3c50a937d7c1 draft

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5:2d023c621bd0

<tool id="PHYLO_pplacer" name="Place aligned sequences" version="1.0.0">
  <description>on a reference tree</description>
  <requirements>
    <requirement type="package">yapp_env</requirement>
  </requirements>
  <macros>
    <import>macros.xml</import>
  </macros>
  <version_command>echo "pplacer $(pplacer --version)"</version_command>
  <command interpreter="bash">
    pplacer-wrapper.sh ${config}
  </command>
  <stdio>
    <expand macro="basic_errors"/>
  </stdio>
  <inputs>
    <param name="refpkg" type="data" format="refpkg" label="Reference package"/>
    <param name="query_seqs" type="data" format="fasta" label="Query alignment"/>
  </inputs>
  <outputs>

This tool places query sequences on a fixed reference phylogenetic tree
according to a reference alignment, producing taxonomic annotations which can
be used for classification and visualization.

-----

**Citation**

Matsen F, Kodner R, Armbrust E V: **pplacer: linear time maximum-likelihood and
Bayesian phylogenetic placement of sequences onto a fixed reference tree**. BMC
Bioinformatics 2010, **11**:1.

  </help>
</tool>

6:3c50a937d7c1

<tool id="PHYLO_pplacer" name="Place aligned sequences" version="1.0.0">
  <description>on a reference tree</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <requirements>
    <requirement type="package">yapp_env</requirement>
  </requirements>
  <stdio>
    <expand macro="basic_errors"/>
  </stdio>
  <version_command>echo "pplacer $(pplacer --version)"</version_command>
  <command interpreter="bash">
    pplacer-wrapper.sh ${config}
  </command>
  <inputs>
    <param name="refpkg" type="data" format="refpkg" label="Reference package"/>
    <param name="query_seqs" type="data" format="fasta" label="Query alignment"/>
  </inputs>
  <outputs>

This tool places query sequences on a fixed reference phylogenetic tree
according to a reference alignment, producing taxonomic annotations which can
be used for classification and visualization.

  </help>
  <citations>
    <expand macro="cite_pplacer"/>
  </citations>
</tool>