view genbank_to_fasta.xml @ 0:bcdd1a35e545 draft default tip

planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty

<tool id ="genbank_to_fasta" name="Convert multigenbank to multifasta" version=" 0.1.0">
    <description></description>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command>python $__tool_directory__/genbank_to_fasta.py "$input" "$output"</command>
    <inputs>
        <param format="txt" name="input" type="data" label="Multigenbank file"/>
    </inputs>
    <outputs>
        <data format="fasta" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="genbank_input.txt"/>
            <output name="output" file="output.fasta"/>
        </test>
    </tests>
    <help>

This tool converts a multigenbank file into a multifasta file.

-----

**Example multi genbank file** ::

    ID   DME9736    standard; DNA; INV; 7411 BP.
    XX
    CC   Derived from AJ009736 (e1371475) (Rel. 58, Last updated, Version 1).
    CC   Takis Benos and Michael Ashburner, 1-Feb-1999.
    CC   Any changes to original sequence record are annotated in an FT line.
    XX
    SQ   Sequence 7411 BP; 3047 A; 1363 C; 1109 G; 1892 T; 0 other;
         GTGACATATC CATAAGTCCC TAAGACTTAA GCATATGCCT ACATACTAAT ACACTTACAA        60
         CACATACACC CCAATACAAC ATACACTACT CCGGATGTAC CCAACAGATA CCAGATAAGA       120
         ATAAGATTGT TATATGATCC TCGAGAATGG AAAAAACCCC AATTCTAGAT AAGTCACCCA       180
         CTGGTAGACT AAACATCCGT CCCCTAATTT AAACAATTCC TTGCTTAAGC CTCACCCCAT       240
    //
    ID   DMIS176    standard; DNA; INV; 7439 BP.
    XX
    CC   Derived from X01472 (g8142) (Rel. 36, Last updated, Version 2).
    CC   Takis Benos and Michael Ashburner, 20-Aug-1997.
    CC   Any changes to original sequence record are annotated in an FT line.
    XX
    SQ   Sequence 7439 BP;  2985 A; 1512 C; 1048 G; 1894 T; 0 other;
         AGTGACATAT TCACATACAA AACCACATAA CATAGAGTAA ACATATTGAA AAGCCGCATA        60
         CGTAAACAAT AAGTGACCAC CATGCTAATG TGGATCAAAT AACAAAAATA TCCACTCTGC       120
    //

**Example output fasta file** ::

   >DME9736
   GTGACATATCCATAAGTCCCTAAGACTTAAGCATATGCCTACATACTAATACACTTACAA....
   >DMIS176
   AGTGACATATTCACATACAAAACCACATAACATAGAGTAAACATATTGAAAAGCCGCATA

    </help>
</tool>