Mercurial > repos > eric-rasche > apollo

<?xml version="1.0"?>
<tool id="edu.tamu.cpt2.webapollo.fetch_jbrowse" name="Retrieve JBrowse" version="3.0">
  <description>for an organism, from Apollo</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <code file="webapollo.py"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
mkdir -p $jbrowse.files_path/;

python $__tool_directory__/fetch_organism_jbrowse.py
@ADMIN_AUTH@

@ORG_OR_GUESS@
$jbrowse.files_path/;

cp $dummyIndex $jbrowse;

]]></command>
  <configfiles>
      <configfile name="dummyIndex">
      <![CDATA[
      <html>
          <head>
          </head>
          <body>
              <h1>JBrowse Data Directory</h1>
              <p>
                Hi! This is not a full JBrowse instance. JBrowse v0.4(+?)
                started shipping with the ability to produce just the
                "data" directory from a JBrowse instance, rather than a
                complete, standalone instance. This was intended to be used
                with the in-development Apollo integration, but may have other
                uses as well.
              </p>
              <p>
                <u>This is not usable on its own</u>. The output dataset may be
                used with Apollo, or may be passed through the "JBrowse -
                Convert to Standalone" tool in Galaxy to "upgrade" to a full
                JBrowse instance.
              </p>
          </body>
      </html>
          ]]>
      </configfile>
  </configfiles>
  <inputs>
    <expand macro="org_or_guess" />
  </inputs>
  <outputs>
    <data format="html" name="jbrowse"/>
  </outputs>
  <help><![CDATA[
**What it does**

Fetches the JBrowse directory from Apollo back into Galaxy.

.. class:: warningmark

If you provide an Apollo JSON file, only the first organism block will be used
in Common Name determination, as it is improbable you wish to apply a single
JBrowse instance to multiple organisms.

@REFERENCES@
]]></help>
</tool>
author	eric-rasche
date	Wed, 01 Mar 2017 22:39:58 -0500
parents	d4ae83dedb14
children	f9a6e151b3b4