comparison alignment.xml @ 6:3c50a937d7c1 draft

Uploaded

5:2d023c621bd0

<tool id="PHYLO_alignment" name="Align query sequences" version="1.0.0">
  <description>with sequences in a reference package</description>
  <requirements>
    <requirement type="package">yapp_env</requirement>
  </requirements>
  <macros>
    <import>macros.xml</import>
  </macros>
  <version_command>echo "guppy $(guppy --version)"</version_command>
  <command interpreter="bash">
    alignment-wrapper.sh ${config}
  </command>
  <stdio>
    <expand macro="basic_errors"/>
  </stdio>
  <inputs>
    <param name="refpkg" type="data" format="refpkg" label="Reference package"/>
    <param name="input_seqs" type="data" format="fasta" label="Input sequences"/>
  </inputs>
  <outputs>

This tool aligns query sequences with the reference sequences used to make the
reference tree contained in the reference package and then merges the query and
reference sequences.

  </help>
</tool>

6:3c50a937d7c1

<tool id="PHYLO_alignment" name="Align query sequences" version="1.0.0">
  <description>with sequences in a reference package</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <requirements>
    <requirement type="package">yapp_env</requirement>
  </requirements>
  <stdio>
    <expand macro="basic_errors"/>
  </stdio>
  <version_command>echo "$(taxit -V); $(cmalign -h | grep INFERNAL); $(esl-alimerge -h | grep Easel)"</version_command>
  <command interpreter="bash">
    alignment-wrapper.sh ${config}
  </command>
  <inputs>
    <param name="refpkg" type="data" format="refpkg" label="Reference package"/>
    <param name="input_seqs" type="data" format="fasta" label="Input sequences"/>
  </inputs>
  <outputs>

This tool aligns query sequences with the reference sequences used to make the
reference tree contained in the reference package and then merges the query and
reference sequences.

  </help>
  <citations>
    <expand macro="cite_taxtastic"/>
    <expand macro="cite_infernal"/>
  </citations>
</tool>