Mercurial > repos > fernando > protein_funcional_analysis_similarities

<tool id="BLaGiFer_2" name="Sequences assortment" version="1.0.0">
    <description> Select the most similar sequences</description>
    <command interpreter="bash">
    ./paso2.sh "$infile" "$outfile" "$numsequences"
    </command>

        <inputs>
            <param name="infile" type="data" format="txt" label="ids file"/>

	     <param name="numsequences" type="select" label="Select number of sequences" help="">
                <option value="1">1</option>
                <option value="2">2</option>
		<option value="3">3</option>
		<option value="4">4</option>
		<option value="5" selected="true">5</option>
            </param>
      </inputs>
<outputs>
<data format="fasta" name="outfile"/>
</outputs>

<stdio><exit_code range="1:" level="fatal" description="Error" /></stdio>
    <help>

**What it does**

From the output text file generated in RemoteBlast wrapper, the user may choose from the five first sequences. The result is stored in a fasta file.

**Dependencies**

This tool only runs UNIX commands, awk is necessary to be installed.


#####
Input
#####

The input text file generated by RemoteBlast is necessary.

######

The Blast results are saved on an output text file.


Example Output
--------------

>sp|Q09443|ARP6_CAEEL Actin-like protein C08B11.6 OS=Caenorhabditis elegans GN=arp-6 PE=2 SV=3
MSLTTIIFDNGGHNMKIGTIDSESPRLVPNSIVKAKHEKKRVFVAHEQEECSDKFSLFYV
RPIERGYVVNWDTQQQIWEKTFGSMDVEASTSRIALTDNNYLIPALPDVSSEILFDYFGF
TEVHKTSASTLVAKHSNKINNEKCAVVVDSGFSWTTVASFVNGMLIQDSVIRIDVGGKAL
TNKLKDWVSYRQLNVSEETYVINECKEDLCFVSQNFDESMKEARNRFQENTTMKRYIMPD
FHSTFRGVVKDVKEPHDPQIPSIHLGVERFAIPEILFNPSDIDIDQCGVAEAVIESICQC
PEALRPALAENIIVIGGSSCFPGFRERLEREVRSMLPAEYGLNVSNDVINPQTHSWHCGQ
ELLTASKVPWINRKDWDERGDSLEFSNFFQTLVQSDELKGTRNFDDQREKSPKEDEDF
>sp|Q9D864|ARP6_MOUSE Actin-related protein 6 OS=Mus musculus GN=Actr6 PE=1 SV=2
MTTLVLDNGAYNAKIGYSHDSVSVIPNCQFRSKTARLKTFTANQIDEIKDPSGLFYILPF
QKGYLVNWDVQRQVWDYLFGKEMYQVDFLDTNIIITEPYFNFTSIQESMNEILFEEYQFQ
AVLRVNAGALSAHRYFRDNPSELCCIIVDSGYSFTHIVPYCRSKKKKEAIIRINVGGKLL
TNHLKEIISYRQLHVMDETHVINQVKEDVCYVSQDFYRDMDIAKLKGEDNTVMIDYVLPD
FSTIKKGFCKPREEMVLSGKYKSGEQILRLANERFAVPEILFNPSDIGIQEMGIPEAIVY
SIQNLPEEMQPHFFKNIVLTGGNSLFPGFRERVYSEVRCLTPTDYDVSVVLPENPITYSW
EGGKLISENDDFEDMVVTREDYEENGHSVCEEKFDI
>sp|Q9GZN1|ARP6_HUMAN Actin-related protein 6 OS=Homo sapiens GN=ACTR6 PE=1 SV=1
MTTLVLDNGAYNAKIGYSHENVSVIPNCQFRSKTARLKTFTANQIDEIKDPSGLFYILPF
QKGYLVNWDVQRQVWDYLFGKEMYQVDFLDTNIIITEPYFNFTSIQESMNEILFEEYQFQ
AVLRVNAGALSAHRYFRDNPSELCCIIVDSGYSFTHIVPYCRSKKKKEAIIRINVGGKLL
TNHLKEIISYRQLHVMDETHVINQVKEDVCYVSQDFYRDMDIAKLKGEENTVMIDYVLPD
FSTIKKGFCKPREEMVLSGKYKSGEQILRLANERFAVPEILFNPSDIGIQEMGIPEAIVY
SIQNLPEEMQPHFFKNIVLTGGNSLFPGFRDRVYSEVRCLTPTDYDVSVVLPENPITYAW
EGGKLISENDDFEDMVVTREDYEENGHSVCEEKFDI
>sp|Q9DEE9|ARP6_CHICK Actin-related protein 6 OS=Gallus gallus GN=ACTR6 PE=2 SV=1
MATLVLDNGAYNAKIGYSHAHVSVIPNCQFRSKTARLKTFTANQLDEIKDPSGLFYILPF
QKGYLVNWDVQRQVWDYLFGKEMYQVDFVDTNIIITEPYFNFSSIQESMNEILFEEYQFQ
AVLRVNAGALSAHRYFRDNPSELCCIIVDSGYSFTHIVPYCRSKKKKEAIIRINVGGKLL
TNHLKEIISYRQLHVMDETHVINQVKEDVCYVSQDFYKDMEIAKLKGEENTVMVDYVLPD
FSTIKKGFCKPREEMVLSGKYKTGEQILRLTNERFAVPEILFHPSDIGIQEMGIPEAIVD
SIQNLPEEMQPHFFKNIVLTGGNTLFPGFRDRVYSEVRCLTPTDYDVSVVLPENPITYSW
EGGKLISENDDFEDLVVTREDYEEHGHNICEEKFDI

**Galaxy Wrapper Authors**::

    * Ginés Almagro
    * Laura Entrambasaguas
    * Fernando Pérez
    </help>
</tool>
author	fernando
date	Thu, 22 May 2014 05:09:07 -0400
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