annotate tools/ncbi_blast_plus/ncbi_makeprofiledb.xml @ 16:b5f1f599d1fb draft

Uploaded v0.1.04, fix regression with BLAST database from history

<tool id="ncbi_makeprofiledb" name="NCBI BLAST+ makeprofiledb" version="0.1.04">
    <description>Make profile database</description>
    <macros>
        <token name="@BINARY@">makeprofiledb</token>
        <import>ncbi_macros.xml</import>
    </macros>
    <expand macro="preamble" />
    <command>
##Unlike makeblastdb, makeprofiledb needs directory to exist already:
mkdir -p $outfile.files_path &amp;&amp;
makeprofiledb -out "${os.path.join($outfile.files_path,'blastdb')}"

##We turn $infile_list into $infiles with a configfile entry defined below
-in $infiles

#if $title:
-title "$title"
#else:
##Would default to being based on the cryptic Galaxy filenames, which is unhelpful
-title "Profile Database"
#end if

-threshold $threshold

#if str($contain_pssm_scores.contain_pssm_scores_type) == 'no':
    -gapopen $contain_pssm_scores.gapopen
    -gapextend $contain_pssm_scores.gapextend
    -scale $contain_pssm_scores.scale
    -matrix $contain_pssm_scores.matrix
#end if

-obsr_threshold $obsr_threshold
-exclude_invalid $exclude_invalid

-logfile "$outfile"
    </command>
    <configfiles>
        <configfile name="infiles">
#for $infile in $input_file
${infile}
#end for
        </configfile>
    </configfiles>
    <inputs>
        <param name="input_file" type="data" multiple="true" optional="false" format="pssm-asn1"
	       label="Input PSSM files(s)"
	       help="One or NCBI PSSM ASN.1 format scoremat files (often named *.smp)" />
        <param name="infile_list" type="data" multiple="true" format="pssm-asn1" />

        <param name="title" type="text" value="" label="Title for the profile database" help="This is the database name shown in BLAST search output" />
        <param name="threshold" type="float" size="5" value="9.82" label="Minimum word score to add a word to the lookup table" />

        <!-- output options -->
        <!-- Initially we're only offering the default, RPS databases for use with rpsblast and rpstblastn
        <param name="dbtype" type="select" display="radio" label="Type of database">
            <option value="cobalt">Cobalt</option>
            <option value="delta">Delta</option>
            <option value="rps" selected="true">RPS</option>
        </param>
        -->

        <conditional name="contain_pssm_scores">
            <param name="contain_pssm_scores_type" type="select" label="Does your input file contain PSSM scores?">
              <option value="yes" selected="True">Yes</option>
              <option value="no">No</option>
            </param>
            <when value="yes" />
            <when value="no">
                <param name="gapopen" type="integer" size="5" value="" label="Cost to open a gap" />
                <param name="gapextend" type="integer" size="5" value="" label="Cost to extend a gap" />
                <param name="scale" type="float" size="5" value="" label="PSSM scale factor" />
                <expand macro="input_scoring_matrix" />
            </when>
        </conditional>

        <!--  Delta Blast Options -->
        <param name="exclude_invalid" type="boolean" truevalue="true" falsevalue="false" checked="true" 
            label="Exclude invalid domains?"
            help="Exclude domains that do not pass validation test" />
        <param name="obsr_threshold" type="float" size="5" value="6.0"
            label="Observation threshold"            
            help="Exclude domains with with maximum number of independent observations below this threshold" />
    </inputs>
    <outputs>
        <data name="outfile" format="blastdbd" label="RPS database from ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="cd00003.smp,cd00008.smp" ftype="pssm-asn1" />
            <param name="title" value="Just 2 PSSM matrices" />
            <param name="contain_pssm_scores_type" value="yes" />
            <output name="out_file" file="empty_file.dat" ftype="blastdbd" >
                <extra_files type="file" value="cd00003_and_cd00008.phr" name="blastdb.phr" />
                <extra_files type="file" value="cd00003_and_cd00008.pin" name="blastdb.pin" lines_diff="2" />
                <extra_files type="file" value="cd00003_and_cd00008.psq" name="blastdb.psq" />
                <extra_files type="file" value="cd00003_and_cd00008.freq" name="blastdb.freq" />
                <extra_files type="file" value="cd00003_and_cd00008.loo" name="blastdb.loo" />
                <extra_files type="file" value="cd00003_and_cd00008.psd" name="blastdb.psd" />
                <extra_files type="file" value="cd00003_and_cd00008.psi" name="blastdb.psi" />
                <extra_files type="file" value="cd00003_and_cd00008.rps" name="blastdb.rps" />
                <extra_files type="file" value="cd00003_and_cd00008.aux" name="blastdb.aux" />
            </output>
        </test>
    </tests>
    <help>
**What it does**

Make a protein domain profile database (for use with RPS-BLAST or RSP-TBLASTN)
from one or more Position Specific Scoring Matrices (PSSM) files in the NCBI
"scoremat" ASN.1 format (usually named ``*.smp``).

This is a wrapper for the NCBI BLAST+ tool 'makeprofiledb'.

More information about makeprofiledb 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:

@REFERENCES@
    </help>
    <expand macro="blast_citations" />
</tool>