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<HTML>
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  <TITLE>
  EMBOSS: urlget
  </TITLE>
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<BODY BGCOLOR="#FFFFFF" text="#000000">

<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
urlget
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Get URLs of data resources
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->




<H2>
    Description
</H2>

Retrieves one or more URLs for further information about an identifier
in a data resource.

<p>
EMBOSS can retrieve specific data types (sequences, features,
taxonomy, resources, ontology terms) as defined ACD types.

<p>
Where there is no defined ACD inpu type, EMBOSS can retrieve the text
of a database entry where the information is provided in a
human-readable text format.

<p>
For many data resources there is no retrievable data format. In these
cases EMBOSS can use the Data Resource Catalogue to construct URLs
that can be viewed in the user's preferred browser which should be
able to render them in a meaningful way.





<H2>
    Algorithm
</H2>

<b>urlget</b> constructs the URL using the information in the Data
Resource Catalogue entry which can be retrieved in its original format
using <b>drget</b>.

<p>
The Query records are searched to find a query that returns HTML data
(not parseable as text). The user-supplied identifier is inserted in
the query to construct a URL.

<p>
If the identifier is specified as a swissprot (<i>-swiss</i>) or EMBL
(<i>-embl</i>) cross-reference the defiitions of swissprot or EMBL
cross-references in the DRCAT entry are used to select queries
matching the identifier type.

<p>
Alternatively, the EDAM term name describing the identifier can be
provided by the user to resolve the selection from multiple queries.

<H2>
    Usage
</H2>

<!--  
	Example usage, as run from the command-line.
        Many examples illustrating different behaviours is good.
 -->

Here is a sample session with <b>urlget</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>urlget pseudocap:PA3363 -swiss </b>
Get URLs of data resources
Url output file [pa3363.url]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#output.1">Go to the output files for this example</a><p><p>



<H2>
    Command line arguments
</H2>

<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Get URLs of data resources
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-url]               url        Url filename and optional format, or
                                  reference (input query)
  [-outfile]           outurl     (no help text) outurl value

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-url" associated qualifiers
   -iformat1           string     Input URL format
   -idbname1           string     User-provided database name
   -swiss1             boolean    Swissprot cross-reference
   -embl1              boolean    EMBL/GenBank/DDBJ cross-reference
   -accession1         string     Primary accession for source data
   -identifier1        string     Identifier term name in EDAM

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory
   -oformat2           string     URL output format

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-url]<br>(Parameter 1)</td>
<td>url</td>
<td>Url filename and optional format, or reference (input query)</td>
<td>URL entries</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-outfile]<br>(Parameter 2)</td>
<td>outurl</td>
<td>(no help text) outurl value</td>
<td>URL entries</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-url" associated url qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -iformat1<br>-iformat_url</td>
<td>string</td>
<td>Input URL format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -idbname1<br>-idbname_url</td>
<td>string</td>
<td>User-provided database name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -swiss1<br>-swiss_url</td>
<td>boolean</td>
<td>Swissprot cross-reference</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -embl1<br>-embl_url</td>
<td>boolean</td>
<td>EMBL/GenBank/DDBJ cross-reference</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -accession1<br>-accession_url</td>
<td>string</td>
<td>Primary accession for source data</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -identifier1<br>-identifier_url</td>
<td>string</td>
<td>Identifier term name in EDAM</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated outurl qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -odirectory2<br>-odirectory_outfile</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -oformat2<br>-oformat_outfile</td>
<td>string</td>
<td>URL output format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>

<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->








<H2>
    Input file format
</H2>

<!-- 
        This includes example input file formats.
        This should be a detailed description and example - assume
        someone will want to parse this file and will want to know what
        happens in unusual cases - null input, etc. 
   -->

<b>urlget</b> reads a query containing a database name from DRCAT and
an identifier.


<p>






<H2>
    Output file format
</H2>

<!-- 
        This includes example output file formats.
        This should be a detailed description and example - assume
        someone will want to parse this file and will want to know what
        happens in unusual cases - null output, errors etc. 

        If you wish to include the standard description of the avalable
	report formats, use:
        #include file="inc/reportformats.ihtml"
   -->

<b>urlget</b> returns a file containing one or more URLs with a description.

<p>
The <i>-oformat</i> qualifier provides a choice of formats which may
be extended in future releases.

<p>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: pa3363.url</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
http://www.pseudomonas.com/getAnnotation.do?locusID=PA3363        Locus ID (PseudoCAP): PA3363
</pre>
</td></tr></table><p>





<H2>
    Data files
</H2>

<b>urlget</b> uses the Data Resource Catalogue to retrieve information
on URLs for the specified database name.


<H2>
    Notes
</H2>

<!-- 
        Restrictions.
        Interesting behaviour.
        Useful things you can do with this program.
   -->

None.







<H2>
    References
</H2>

<!-- 
        Bibliography for methods used.
<ol>

<li>

</ol>

   -->

None.








<H2>
    Warnings
</H2>

<!-- 
        Potentially stupid things the program will let you do.
   -->

None.







<H2>
    Diagnostic Error Messages
</H2>

<!-- 
        Error messages specific to this program, eg:
        "FATAL xxx" - means you have not set up the xxx data using program <b>prog</b>.<p>
   -->

None.







<H2>
    Exit status
</H2>

<!-- 
        Description of the exit status for various error conditions
   -->

It always exits with status 0.








<H2>
    Known bugs
</H2>


<!-- 
        Bugs noted but not yet fixed.
   -->

None.








<!--
<H2>
    See also
</H2>
-->
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th>
<th>Description</th></tr>
</table>
<!-- 
        Add any comments about other associated programs (to prepare
        data files?) that seealso doesn't find. 
   -->










<H2>
    Author(s)
</H2>
Peter Rice
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.


<H2>
    History
</H2>
<!--
        Date written and what changes have been made go in this file.
   -->




<H2>
    Target users
</H2>
<!--
        For general users, use this text
   -->
This program is intended to be used by everyone and everything, from naive users to embedded scripts.

<H2>
    Comments
</H2>
<!--
        User/developer/other comments go in this file.
   -->
None


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