<!-- 
# =====================================================
# $Id: ExtractSeqsFromFasta.xml 90 2011-01-19 13:20:31Z pieter.neerincx@gmail.com $
# $URL: https://trac.nbic.nl/svn/galaxytools/trunk/tools/general/FastaTools/ExtractSeqsFromFasta.xml $
# $LastChangedDate: 2011-01-19 07:20:31 -0600 (Wed, 19 Jan 2011) $ 
# $LastChangedRevision: 90 $
# $LastChangedBy: pieter.neerincx@gmail.com $
# =====================================================
-->
<tool id="ExtractSeqsFromFasta1" version="1.1" name="ExtractSeqsFromFasta">
  <description>Extract sequences from a FASTA file based on a list of IDs</description>
  <command interpreter="perl">ExtractSeqsFromFasta.pl $ignore_accession_number_versions -f $identifiers -i $input -o $output -l WARN</command>
  <inputs>
    <param format="fasta" name="input" type="data" label="FASTA sequences"/>
    <param format="txt" name="identifiers" type="data" label="List of IDs to extract sequences for"/>
    <param name="ignore_accession_number_versions" type="boolean" truevalue="-u" falsevalue="" optional="true" label="Ignore accession number versions"/>
  </inputs>
  <outputs>
    <data format="fasta" name="output" label="FASTA sequences for ${identifiers.name}"/>
  </outputs>
<!--
  <tests>
    <test>
      <param name="input"       value="*.fasta"/>
      <param name="identifiers" value="*.txt"/>
      <output name="output"     file="*.fasta"/>
    </test>
  </tests>
-->
  <help>

.. class:: infomark

**What it does**

This tool filters a set of FASTA sequences for certain identifiers (IDs) or accession numbers. \
Only sequences whose ID or accession number is present in the supplied list will remain in the filtered FASTA output. \
The list of IDs or accession numbers to filter for must be a flat text file with one ID or accession per line.

This tool can match IDs with and without colon prefixed database namespaces in FASTA sequence header line. \
Hence your FASTA header can contain both &gt;UniProtKB:Q86Y46 ... or just plain &gt;Q86Y46 ... . \
Database namespace prefixes should not be present in the list of IDs that you want to extract sequences for.

FASTA headers may contain multiple IDs separated with pipe symbols (|) or semi colons (;). \
If multiple IDs are supplied these should not contain any white space as everything after the \
first white space is considered to be the (optional) description, which will not be matched against the list \
of IDs to extract.

If your FASTA file contains versioned IDs / accessions, your list of IDs / accessions to extract must also contain \
versioned IDs / accessions and the version numbers must match.

-----

**Example**

If the FASTA header is this::

   &gt;IPI:CON_IPI00174775.2|TREMBL:Q32MB2;Q86Y46 Tax_Id=9606 Gene_Symbol=KRT73 Keratin-73

The following IDs / accession numbers will match this sequence header::

   CON_IPI00174775.2
   Q32MB2
   Q86Y46

These will not match::

   IPI:CON_IPI00174775.2 (prefix should be removed)
   KRT73                 (ID part of description and not part of list of IDs, 
                          which is everything up until the first white space.)

And finally these will not match unless *ignore accession number versions* is enabled::

   CON_IPI00174775       (no version number, while FASTA file does contain versioned accession numbers)
   CON_IPI00174775.1     (wrong version number)

  </help>
</tool>