convert_gsMapper_gff3.xml

<?xml version="1.0"?>
<tool id="gsMapper_to_gff3_1" name="Convert gsMapper to gff3">
  <description>Convert Roche gsMapper to GFF3</description>
  <command interpreter="bash">gsmapper2gff.sh  $inputGsFile  $outputfile</command>
  <inputs>
    <param format="txt" name="inputGsFile" type="data" label="Roche gsMapper 454HCDiffs.txt or 454AllDiffs.txt file"/>

  </inputs>
  <outputs>
     <data format="gff3" name="outputfile" />
  </outputs>
<help>
.. class:: infomark

**TIP**

This tool parses Roche gsMapper read mapping output into GVF/GFF3 format


----

**Example**

*input*

::

 >Reference      Start   End     Ref     Var     Total   Var     Ref     Var     Coding  Region  Known   # Fwd   # Rev   # Fwd   # Rev
 >Accno           Pos    Pos     Nuc     Nuc     Depth   Freq    AA      AA      Frame   Name    SNP's   w/ var  w/ var  Total   Total
 ______________________________

 >1118212        673     673     A       C       7       100%                                            6       1       6       1
 
 Reads with Difference:
 1118212                     648+ GTTGGTCCACTATTACTCTCAGATT-ATTTCATAACAATAATGG----A-TAC-AA 696
                                                           **
 FX289JP01DVQR7               53- GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATAATGGGCTGA-TACTA  1
 FX289JP02IJT2O  (7)          82+ GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATAATGG----A-TAC-AA 130
 FX289JP01B8R7V               84+ GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATA-TGG----A-TAC-AA 131
 FX289JP02FX58L               68+ GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATAATGG----AC-AC-AA 116
 FX289JP02JXAX7  (7)          67+ GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATAATGG----A-TAC-AA 115
 FX289JP02JOOQZ  (2)          69+ GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATAATGG----A-TAC-AA 117
 FX289JP02GPHPX               45+ GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATAATGG----A-TAC-AA 93
                                                          **


*output*

::

 ##gff-version 3
 1118212 gsMapper SNP 673 673 . . . ID=1118212:gsMapper:SNP:673;Reference_seq=A;Variant_seq=C;Total_reads=7;Variant_freq=100;
 1118212 gsMapper SNP 730 730 . . . ID=1118212:gsMapper:SNP:730;Reference_seq=A;Variant_seq=G;Total_reads=13;Variant_freq=31;
 1118212 gsMapper SNP 782 782 . . . ID=1118212:gsMapper:SNP:782;Reference_seq=T;Variant_seq=C;Total_reads=13;Variant_freq=92;
 1118212 gsMapper SNP 1319 1319 . . . ID=1118212:gsMapper:SNP:1319;Reference_seq=G;Variant_seq=A;Total_reads=7;Variant_freq=100;

-----------------------

*If you use this tool please cite:*

A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data: 
Application For  Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
(2012)

Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, 
Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum

 
</help>
</tool>