annotate tool_dependencies.xml @ 0:eaadf9edc5c1 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_art_2014_11_03 commit 44c7d88ebdbf798890394a7696a4ce0c504faaf7

<?xml version="1.0"?>
<tool_dependency>
  <package name="package_gsl_1_16" version="1.16">
    <repository changeset_revision="4391a79f86fa" name="package_gsl_1_16" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="art" version="2014_11_03">
    <install version="1.0">
      <actions>
        <action type="download_by_url">http://www.niehs.nih.gov/research/resources/assets/docs/artsrcvanillaicecream031114linuxtgz.tgz</action>
        <action type="set_environment_for_install">
          <repository changeset_revision="4391a79f86fa" name="package_gsl_1_16" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
            <package name="gsl" version="1.16" />
          </repository>
        </action>
        <action type="autoconf" />
        <action type="set_environment">
          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable>
          <environment_variable action="set_to" name="ART_ROOT_PATH">$INSTALL_DIR/</environment_variable>
        </action>
      </actions>
    </install>
    <readme>ART is a set of simulation tools to generate synthetic next-generation
sequencing reads. ART simulates sequencing reads by mimicking real
sequencing process with empirical error models or quality profiles summarized
from large recalibrated sequencing data. ART can also simulate reads using user
own read error model or quality profiles. ART supports simulation of
single-end, paired-end/mate-pair reads of three major commercial
next-generation sequencing platforms: Illumina's Solexa, Roche's 454 and
Applied Biosystems' SOLiD. ART can be used to test or benchmark a variety
of method or tools for next-generation sequencing data analysis, including
read alignment, de novo assembly, SNP and structure variation discovery.
ART was used as a primary tool for the simulation study of the 1000 Genomes
Project . ART is implemented in C++ with optimized algorithms and is highly
efficient in read simulation. ART outputs reads in the FASTQ format, and
alignments in the ALN format. ART can also generate alignments in the SAM
alignment or UCSC BED file format.
</readme>
  </package>
</tool_dependency>