<!-- 
# =====================================================
# $Id: ExtractPeptideSequenceContext.xml 90 2011-01-19 13:20:31Z pieter.neerincx@gmail.com $
# $URL: https://trac.nbic.nl/svn/galaxytools/trunk/tools/general/FastaTools/ExtractPeptideSequenceContext.xml $
# $LastChangedDate: 2011-01-19 07:20:31 -0600 (Wed, 19 Jan 2011) $ 
# $LastChangedRevision: 90 $
# $LastChangedBy: pieter.neerincx@gmail.com $
# =====================================================
-->
<tool id="ExtractPeptideSequenceContext1" version="0.1" name="Extract Peptide Context">
  <description>by mapping peptides back to proteins and extending them on both termini to include their sequence context.</description>
  <command interpreter="perl">ExtractPeptideSequenceContext.pl --db $db --dbf FASTA --f $fragments --icol $icol --pcol $pcol $strip --pepo $pepo --n $n --c $c --pc '$pc' --ll WARN</command>
  <inputs>
    <param name="fragments"     type="data" format="tabular"    label="Peptide sequences and their protein's identifiers"
           help="(in tab delimited format)"/>
    <param name="icol" type="data_column" value="1" data_ref="fragments" label="Protein identifier column"/>
    <param name="pcol" type="data_column" value="2" data_ref="fragments" label="Peptide sequence column"/>
    <!--
    <param name="icol" type="integer" value="1" label="Protein identifier column"/>
    <param name="pcol" type="integer" value="2" label="Peptide sequence column"/>
    -->
    <param name="strip" type="select">
      <label>Lowercase characters in the peptide sequences represent</label>
      <option value="--s">Modifications</option>
      <option value="">Amino acids</option>
    </param>
    <param name="db"            type="data" format="fasta"      label="Protein sequences"
           help="(in FASTA format)"/>
    <param name="n"	type="integer"	value="5"		label="N-terminal sequence context length"/>
    <param name="c"	type="integer"	value="5"		label="C-terminal sequence context length"/>
    <param name="pc"	type="select" help="to fill positions in the sequence context when the protein was too short for a full length context.">
      <label>Padding character</label>
      <option value="-">dash</option>
      <option value=" ">space</option>
      <option value="">none</option>
    </param>
  </inputs>
  <outputs>
    <data name="pepo" format="tabular" label="Peptide sequence contexts for ${fragments.name}"/>
  </outputs>
<!--
  <tests>
    <test>
      <param name="input"       value="*.fasta"/>
      <param name="identifiers" value="*.txt"/>
      <output name="output"     file="*.fasta"/>
    </test>
  </tests>
-->
  <help>

.. role:: raw-html(raw)
   :format: html

.. class:: infomark

**What it does**

Map peptide sequences back to proteins and extend the peptides on both termini to include their sequence context.

:raw-html:`&lt;object data="static/images/nbic_gmr/ExtractPeptideSequenceContext.svg" type="image/svg+xml" width="100%"/&gt;`

===================================================
*Peptide sequences and their protein's identifiers*
===================================================

This file must contain at least peptides and accession numbers or IDs of the proteins the peptides were derived from. \
The data must be in TAB delimited format and may contain other columns, which will be preserved in the output. \
If a sequence context was found, it will be appended in a new column to the right of the existing columns. \
When another sequence context was found for the same peptide, it will appended as an extra row in the output.
Protein accession numbers / IDs must be in the same format as was used in the FASTA file with protein sequences (database). \
The only exception to this rule is that accession numbers / IDs may be optionally suffixed with the peptide\'s position in its protein between brackets. \	
For example: CLH1_HUMAN[1612-1620] will be matched to CLH1_HUMAN in a FASTA file with protein sequences. \
Amino acids in the petide sequences must be in uppercase.

===============================================
*Protein sequences*
===============================================

Input file containing all protein sequences in FASTA format. \
This tool will look for any type of protein ID in the first part of FASTA sequence headers up until the first white space. \
Optionally multiple IDs may be present separated with pipe symbols (|) or semicolons (;). \
Optionally IDs may be prefixed with a database namespace and a colon (:). \
For example the accession number P32234 as well as the ID 128UP_DROME would be recognized in both this sequence header: 

   >UniProtAcc:P32234|UniProtID:128UP_DROME GTP-binding protein 128up - Drosophila melanogaster (Fruit fly)

and in this one:

   >P32234|128UP_DROME GTP-binding protein 128up - Drosophila melanogaster (Fruit fly)

===================================================
*N-terminal and C-terminal sequence context length*
===================================================

Integers specifying the length of the N-terminal and C-terminal sequence context to retrieve starting from the peptide termini. \
So the total sequence context length for a peptide will be: 
(N-terminal sequence context) + (length of the peptide) + (C-terminal sequence context).

===============================================
*Padding character*
===============================================

Optional padding character to fill N-terminal or C-terminal positions in the sequence context, \
when the protein was too short to get a complete sequence context. \
Defaults to - a.k.a. dash or alignment gap character. \

-----
 
**Getting input data** 

.. _my folder utility: http://mascotinternal.chem.uu.nl/mascot/cgi/uu_myfolder.pl

This tool requires \
peptide sequences in TAB delimited format and \
protein sequences from which the peptides were derived in FASTA format. \
If your peptide sequences are not in TAB delimited format, you can convert from:
 
 - FASTA format using *FASTA manipulation* -&gt; *FASTA-to-Tabular* 
 - A format using a different delimiter using *Text Manipulation* -&gt; *Convert*
 
When your peptides were derived from a mass spectrometry experiment and identified with a search engine like Mascot, Sequest, etc.,\
please make sure you provide the same FASTA database for this tool as the one used for your search.
If you used Mascot hosted by the Biomolecular Mass Spectrometry and Proteomics Group @ Utrecht University, \
you can use the `my folder utility`_ to download the FASTA databases from the Mascot server.  

-----

**Examples**

Example input for peptides identified with a Mascot search, \
some with phosphorylated residues indicated by pS, pT or pY \
and in TAB delimited format::

   sequence	    score   peptide mr   mass delta (abs)   mass delta (ppm)       all protein matches
   AGNAARDN     54.24   787.357254   -4.223E-5          -0.05334300253990      H2A1B_HUMAN[67-74]
   KLpSAAVVLI   11.48   912.600784   0.001608           1.7619971713721432     OSGI2_HUMAN[405-413]
   RAGIKVpTVA   23.01   913.570892   6.283E-5           0.06786555979719196    PARK7_HUMAN[28-36]
   KGGVVGIKVD   44.61   970.581146   -0.001214          -1.2507970147608864    P04075[101-110]
   KIKELQAF     11.87   975.575287   0.003907           4.00481649347068       O60882[71-78]
   KIpSGpTVNIR  57.17   986.587265   -0.002761          -2.798536022051734     SYTC_HUMAN[681-689]
   KLpYEALKF    17.54   1010.580032  0.004782           4.731935966057164      F105A_HUMAN[238-245]
   KLDApSEpSLR  31.31   1017.545441  -0.002377          -2.3360136110127785    CLH1_HUMAN[1612-1620]

===============================================
*Appending peptide sequence contexts*
===============================================

With these options:

 - c6 as *Protein identifier column*
 - c1 as *Peptide sequence column*
 - 5 as *N-terminal sequence context length* 
 - 5 as *C-terminal sequence context length*
 - a suitable FASTA database with *Protein sequences*
 - and everything else set to defaults

the example above will generate a result like this::

   AGNAARDN     54.24   787.357254   -4.223E-5          -0.05334300253990      H2A1B_HUMAN[67-74]     EILELAGNAARDNKKTRI
   KLpSAAVVLI   11.48   912.600784   0.001608           1.7619971713721432     OSGI2_HUMAN[405-413]   LKKIFKLSAAVVLIGSHPN
   RAGIKVpTVA   23.01   913.570892   6.283E-5           0.06786555979719196    PARK7_HUMAN[28-36]     VDVMRRAGIKVTVAGLAGK
   KGGVVGIKVD   44.61   970.581146   -0.001214          -1.2507970147608864    P04075[101-110]        QVIKSKGGVVGIKVDKGVVP
   KIKELQAF     11.87   975.575287   0.003907           4.00481649347068       O60882[71-78]          NSMIRKIKELQAFFGLQV
   KIpSGpTVNIR  57.17   986.587265   -0.002761          -2.798536022051734     SYTC_HUMAN[681-689]    VGEKEKISGTVNIRTRDNK
   KLpYEALKF    17.54   1010.580032  0.004782           4.731935966057164      F105A_HUMAN[238-245]   AILEYKLYEALKFIMLYQ
   KLDApSEpSLR  31.31   1017.545441  -0.002377          -2.3360136110127785    CLH1_HUMAN[1612-1620]  LTKVDKLDASESLRKEEEQ

Note the header line was ignored.

  </help>
</tool>