Mercurial > repos > gga > apollo_fetch_jbrowse

<?xml version="1.0"?>
<tool id="fetch_jbrowse" name="Retrieve JBrowse" version="3.3" profile="16.04">
  <description>for an organism, from Apollo</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <code file="webapollo.py"/>
  <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/

"$__user_email__" &&

cp $dummyIndex $jbrowse &&
find $jbrowse.files_path -type f -printf '<li><a href="%P">%P</a></li>\n' | sort >> $jbrowse &&
echo '</ul></body></html>' >> $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>
              <p>
                  The following list is provided for your convenience / debugging.
              </p>
              <h2>Contained Files</h2>
              <ul>
          ]]>
      </configfile>
  </configfiles>
  <inputs>
    <expand macro="org_or_guess" />
  </inputs>
  <outputs>
    <data format="html" name="jbrowse">
        <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
    </data>
  </outputs>
  <tests>
      <test expect_failure="true">
          <conditional name="org_source">
              <param name="source_select" value="direct"/>
              <param name="org_raw" value="Test org" />
          </conditional>
          <expand macro="test_result" />
      </test>
  </tests>
  <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>
  <expand macro="citations"/>
</tool>
author	gga
date	Wed, 10 Apr 2019 13:52:10 -0400
parents	1a2976c6b161
children	d8bb1f9b85b2