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Initial commit.

<!-- 
# =====================================================
# $Id: ExtractModificationSiteSequenceContext.xml 90 2011-01-19 13:20:31Z [e-mail] $
# $URL: https://trac.nbic.nl/svn/galaxytools/trunk/tools/general/FastaTools/ExtractModificationSiteSequenceContext.xml $
# $LastChangedDate: 2011-01-19 07:20:31 -0600 (Wed, 19 Jan 2011) $ 
# $LastChangedRevision: 90 $
# $LastChangedBy: [e-mail] $
# =====================================================
-->
<tool id="ExtractPeptideSequenceContext4" version="2.1" name="Extract Modification Site Context">
  <description>by mapping modified amino acids in peptides back to proteins and fetching the sequence surrounding the modified sites.</description>
  <command interpreter="perl">ExtractPeptideSequenceContext.pl --db $db --dbf FASTA --f $fragments --icol $icol --pcol $pcol --s --modo $modo --ma '$ma' --n $n --c $c --pc '$pc' --ll ERROR</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="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>
    <param name="ma"	type="text"		label="Modified amino acid"/>
  </inputs>
  <outputs>
    <data name="modo" format="tabular" label="Modification site 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 extract sequence contexts for modification sites.

:raw-html:`&lt;object data="static/images/nbic_gmr/ExtractModificationSiteSequenceContext.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 modification site. \
Note that the width of a modification site is 1 amino acid. \
When defaults are used for both the N-terminal and C-terminal sequence context lengths, \
the total sequence context length for a modification site will be: 
(N-terminal sequence context) + (modified amino acid) + (C-terminal sequence context) = 5 + 1 + 5 = 11.
    
===============================================
*Modified amino acid*
===============================================

The amino acid must be specified in uppercase and the modification in lower case. \
The order is not important. \
Hence a phophorylated serine in a peptide sequence can be indicated with either pS or Sp, \
but you cannot mix both pS and Sp in a single peptide sequence file. \
You may provide an asterisk (*) instead of an upper case amino acid to retrieve sequence contexts \
for the specified modification no matter what amino acid it was located on. \
A modification may be specified with more than one lower case character, \
so for example phosphoS or Sphospho can also be used for a phosphorylated serine.

===============================================
*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          -0.05334300253998803   H2A1B_HUMAN[67-74]; H2A1C_HUMAN[67-74]; H2A1D_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    ALDOA_HUMAN[101-110]
   KIKELQAF     11.87   975.575287   0.003907           4.004816493470687      MMP20_HUMAN[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 modification site sequence contexts*
===============================================

With these options:

 - p\* as *modified amino acid* 
 - c6 as *Protein identifier column*
 - c1 as *Peptide sequence column*
 - a suitable FASTA database with *Protein sequences*
 - and everything else set to defaults

the example above will generate a result like this::

   KLpSAAVVLI   11.48   912.600784   0.001608           1.7619971713721432     OSGI2_HUMAN[405-413]   KIFKLSAAVVL
   RAGIKVpTVA   23.01   913.570892   6.283E-5           0.06786555979719196    PARK7_HUMAN[28-36]     AGIKVTVAGLA
   KIpSGpTVNIR  57.17   986.587265   -0.002761          -2.798536022051734     SYTC_HUMAN[681-689]    EKEKISGTVNI
   KIpSGpTVNIR  57.17   986.587265   -0.002761          -2.798536022051734     SYTC_HUMAN[681-689]    EKISGTVNIRT
   KLpYEALKF    17.54   1010.580032  0.004782           4.731935966057164      F105A_HUMAN[238-245]   LEYKLYEALKF
   KLDApSEpSLR  31.31   1017.545441  -0.002377          -2.3360136110127785    CLH1_HUMAN[1612-1620]  DKLDASESLRK
   KLDApSEpSLR  31.31   1017.545441  -0.002377          -2.3360136110127785    CLH1_HUMAN[1612-1620]  LDASESLRKEE

Note the header line was ignored, peptides like AGNAARDN without any modified amino acids are absent from the output \
and peptides like KLDApSEpSLR with more than one modified amino acid occur more than once in the output.

  </help>
</tool>