view tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml @ 13:623f727cdff1 draft

Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.

<tool id="ncbi_convert2blastmask_wrapper" name="NCBI BLAST+ convert2blastmask" version="0.1.00">
    <description>Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb</description>
    <macros>
        <token name="@BINARY@">convert2blastmask</token>
        <import>ncbi_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
convert2blastmask
-in $infile
-masking_algorithm "$masking_algorithm"
-masking_options "$masking_options"
$parse_seqids
-out "$outfile"
-outfmt $outformat
    </command>
    <expand macro="stdio" />
    <inputs>
        <param name="infile" type="data" format="fasta" label="masked FASTA file"/> 
        <param name="masking_algorithm" type="select" label="Used masking algorithm">
            <option value="dust">DUST</option>
            <option value="seg" selected="true">SEG</option>
            <option value="windowmasker">windowmasker</option>
            <option value="repeat">repeat</option>
            <option value="other">other</option>
        </param>
        <param name="masking_options" type="text" value="" size="20" label="Masking algorithm options to create the masked input" 
            help ="free text to describe the options used to create the masking files. (-masking_options)">
            <sanitizer invalid_char="">
                <valid initial="string.printable" />
            </sanitizer>
        </param>
        <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="true" label="Parse Seq-ids in FASTA input" help="(-parse_seqids)" />
        <param name="outformat" type="select" label="Output format">
            <option value="maskinfo_asn1_bin">maskinfo ASN.1 binary</option>
            <option value="maskinfo_asn1_text" selected="True">maskinfo ASN.1 text</option>
            <option value="maskinfo_xml">maskinfo_xml</option>
        </param>
    </inputs>
    <outputs>
        <data name="outfile" format="maskinfo-asn1" label="SEG Masked File">
            <change_format>
                <when input="outformat" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" />
		<!--
                <when input="outformat" value="maskinfo_asn1_text" format="maskinfo-asn1" />
		-->
                <when input="outformat" value="maskinfo_xml" format="xml" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="four_human_proteins_masked.fasta" ftype="fasta" />
            <param name="masking_algorithm" value="seg" />
            <param name="masking_options" value="window=12; locut=2.2; hicut=2.5" />
            <param name="parse_seqids" value="True" />
            <param name="outformat" value="maskinfo_asn1_bin" />
            <output name="outfile" file="convert2blastmask_four_human_masked.maskinfo-asn1-binary" />
        </test>
        <test>
            <param name="infile" value="four_human_proteins_masked.fasta" ftype="fasta" />
            <param name="masking_algorithm" value="seg" />
            <param name="masking_options" value="window=12; locut=2.2; hicut=2.5" />
            <param name="parse_seqids" value="True" />
            <param name="outformat" value="maskinfo_asn1_text" />
            <output name="outfile" file="convert2blastmask_four_human_masked.maskinfo-asn1" />
        </test>
    </tests>
    <help>
**What it does**

Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb.

More information about segmasker can be found in the `BLAST Command Line Applications User Manual`_.

.. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/

**References**

If you use this Galaxy tool in work leading to a scientific publication please
cite the following papers (a more specific paper covering this wrapper is planned):

@REFERENCES@
    </help>
</tool>