<?xml version="1.0"?>
<tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="36">
    <description>BLAST-like sequence alignment tool</description>
    <requirements>
      <requirement type="package" version="36">blat</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
      #if str($reference_source.reference_source_selector) == "history":
            ## blat depends on file extension
            #if $reference_source.database.is_of_type("fasta"):
                #set $reference_fasta_filename = "localref.fa"
            #elif $reference_source.database.is_of_type("twobit"):
                #set $reference_fasta_filename = "localref.2bit"
            #else
                #set $reference_fasta_filename = "localref"
            #end if

            ln -s '${reference_source.database}' '${reference_fasta_filename}' &&
      #else:
            #set $reference_fasta_filename = str($reference_source.database.fields.path)
      #end if

      blat

            -q=$query_type
            -t=$database_type

            ${oneOff}

            #if str($minScore)
              -minScore=${minScore}
            #end if

            -maxGap=${maxGap}

            #if str($repMatch)
              -repMatch=${repMatch}
            #end if

            #if $mask_type.mask == "file.out":
                  -mask='${mask_type.mask_file}'
            #else:
                  -mask=$mask_type.mask
            #end if

            #if str($dots)
              -dots=${dots}
            #end if

            ${trimT}
            ${noTrimA}
            ${trimHardA}
            ${fastMap}
            ${fine}

            #if str($maxIntron)
             -maxIntron=${maxIntron}
            #end if

            ${extendThroughN}

            '$reference_fasta_filename'
            '${query}'

            -out=${out}

            '${output}'
]]></command>
      <inputs>
            <conditional name="reference_source">
                  <param name="reference_source_selector" type="select" label="Choose the source for the database">
                        <option value="cached">Locally cached</option>
                        <option value="history">History</option>
                  </param>
                  <when value="cached">
                        <param name="database" type="select" label="Select database">
                              <options from_data_table="all_fasta">
                                    <filter type="sort_by" column="2" />
                              </options>
                              <validator type="no_options" message="A built-in database is not available" />
                        </param>
                  </when>
                  <when value="history">
                        <param name="database" type="data" format="fasta, twobit" label="Using database file, either a .fa, .nib or .2bit file" />
                  </when>
            </conditional>
            <param type="data" name="query" format="fasta, twobit" label="Query data, either a .fa, .nib or .2bit file"/>
            <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dnax" argument="-t">
                  <option value="dna">dna - DNA sequence</option>
                  <option value="prot">prot - protein sequence</option>
                  <option value="dnax" selected="true">dnax - DNA sequence translated in six frames to protein</option>
            </param>
            <param type="select" name="query_type" format="text" multiple="false" label="query type" help="Choose your query type, the default is rnax" argument="-q">
                  <option value="dna">dna - DNA sequence </option>
                  <option value="rna">rna - RNA sequence</option>
                  <option value="prot">prot - protein sequence</option>
                  <option value="dnax">dnax - DNA sequence translated in six frames to protein</option>
                  <option value="rnax" selected="true">rnax - DNA sequence translated in three frames to protein</option>
            </param>
            <param argument="-oneOff" type="boolean" truevalue="-oneOff=1" falsevalue="" label="If set, this allows one mismatch in tile and still triggers an alignments" />
            <param argument="-minScore" type="integer" value="30" label="Minimum score" help="It is the matches minus the mismatches minus some sort of gap penalty" />
            <param argument="-maxGap" type="integer" value="2" min="0" max="3" label="Maximum gap between tiles in a clump" help="Usually set from 0 to 3. Only relevant for minMatch > 1" />
            <param argument="-repMatch" type="integer" value="" optional="true" label="Number of repetitions of a tile allowed before it is marked as overused" help="Typically this is 256 for tileSize 12, 1024 for tileSize 11, 4096 for tileSize 10. Also affected by stepSize. When stepSize is halved repMatch is doubled to compensate" />
            <conditional name="mask_type">
                  <param name="mask" type="select" label="Mask out repeats" help="Alignments won't be started in masked region
                  but may extend through it in nucleotide searches.  Masked areas
                  are ignored entirely in protein or translated searches. Default is lower" argument="-mask">
                        <option value="lower" selected="true">lower - mask out lower-cased sequence</option>
                        <option value="upper">upper - mask out upper-cased sequence</option>
                        <option value="out">out - mask according to database.out RepeatMasker .out file</option>
                        <option value="file.out">file.out - mask database according to RepeatMasker file.out</option>
                  </param>
                  <when value="lower" />
                  <when value="upper" />
                  <when value="out" />
                  <when value="file.out">
                        <param name="mask_file" type="data" format="txt" label="RepeatMasker file.out" />
                  </when>
            </conditional>
            <param argument="-dots" type="integer" value="" optional="true" label="Output a dot every N sequences in log" help="Dots show program's progress" />
            <param argument="-trimT" type="boolean" truevalue="-trimT" falsevalue="" label="Trim leading poly-T" />
            <param argument="-noTrimA" type="boolean" truevalue="-noTrimA" falsevalue="" label="Don't trim trailing poly-A" />
            <param argument="-trimHardA" type="boolean" truevalue="-trimHardA" falsevalue="" label="Remove poly-A tail from qSize and alignments in .psl output" />
            <param argument="-fastMap" type="boolean" truevalue="-fastMap" falsevalue="" label="Run for fast DNA/DNA remapping" help="It does not allow introns and require high %ID. Query sizes must not exceed 5000" />
            <param argument="-fine" type="boolean" truevalue="-fine" falsevalue="" label="Refine search for small initial and terminal exons" help="For high-quality mRNAs. Not recommended for ESTs" />
            <param argument="-maxIntron" type="integer" value="750000" optional="true" label="Maximum intron size" />
            <param argument="-extendThroughN" type="boolean" truevalue="-extendThroughN" falsevalue="" label="Allow extension of alignment through large blocks of N's" />
            <param name="out" type="select" label="Select output file format (-out)">
                <option value="psl">Tab-separated format, no sequence (psl)</option>
                <option value="psl -noHead">Tab-separated format, no sequence, no header (psl -noHead)</option>
                <option value="axt">Blastz-associated axt format (axt)</option>
                <option value="maf">Multiz-associated maf format (maf)</option>
                <option value="sim4">Similar to sim4 format (sim4)</option>
                <option value="wublast">Similar to WU-BLAST format (wublast)</option>
                <option value="blast">Similar to NCBI BLAST format (blast)</option>
                <option value="blast8">NCBI BLAST tabular format (blast8)</option>
                <option value="blast9">NCBI BLAST tabular format with comments (blast9)</option>
            </param>
      </inputs>
      <outputs>
            <data name="output" format="tabular" label="${tool.name} on ${on_string}">
                <change_format>
                    <when input="out" value="psl" format="psl" />
                    <when input="out" value="axt" format="axt" />
                    <when input="out" value="maf" format="maf" />
                    <when input="out" value="sim4" format="txt" />
                    <when input="out" value="wublast" format="txt" />
                    <when input="out" value="blast" format="txt" />
                </change_format>
            </data>
      </outputs>
  <tests>
      <!-- test on query of GenBank RefSeq records for Gallus gallus and database of Amazona vittata -->
      <test>
            <param name="reference_source_selector" value="history" />
            <param name="database" value="amaVit1_Gallus/amaVit1.fa" />
            <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" />
            <param name="database_type" value="dnax" />
            <param name="query_type" value="rnax" />
            <param name="mask" value="lower" />
            <param name="out" value="psl -noHead" />
            <output name="output" value="amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.psl" sort="True"/>
      </test>
      <!-- test on query of partial mRNA of Drosophila melanogaster and the database of Drosophila biamipes dot chromosome -->
      <test>
            <param name="reference_source_selector" value="history" />
            <param name="database" value="dbia3/dbia3.fa" />
            <param name="query" value="dbia3/dmel-transcript.fa" />
            <param name="database_type" value="dnax" />
            <param name="query_type" value="rnax" />
            <param name="mask" value="lower" />
            <param name="out" value="psl -noHead" />
            <param name="maxIntron" value="" />
            <output name="output" value="dbia3/dbia3.sorted.psl" sort="True"/>
      </test>
      <!-- test on the database masked by repeat masker -->
      <test>
            <param name="reference_source_selector" value="history" />
            <param name="database" value="dbia3/dbia3_masked.2bit" />
            <param name="query" value="dbia3/dmel-transcript.fa" />
            <param name="database_type" value="dnax" />
            <param name="query_type" value="rnax" />
            <param name="oneOff" value="false" />
            <param name="minScore" value="30" />
            <param name="maxGap" value="2" />
            <param name="trimT" value="false" />
            <param name="noTrimA" value="false" />
            <param name="fine" value="false" />
            <param name="maxIntron" value="750000" />
            <param name="extendThroughN" value="false" />
            <param name="mask" value="file.out" />
            <param name="mask_file" value="dbia3/dbia3_RM.out" />
            <param name="out" value="psl -noHead" />
            <output name="output" value="dbia3/dbia3_masked.sorted.psl"/>
      </test>

  </tests>
  <help>
        <![CDATA[
BLAT
====
BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments.

blat (version: v36)- Standalone blat sequence search command line tool.
-------------------------------------------------------------------------

usage:
++++++

  $ blat database query [-ooc=11.ooc] output.psl

where:
   database and query are each either a .fa, .nib or .2bit file,
   or a list of these files with one file name per line.
   -ooc=11.ooc tells the program to load over-occurring 11-mers from
   an external file.  This will increase the speed
   by a factor of 40 in many cases, but is not required.
   output.psl is the name of the output file.

documentation:
++++++++++++++

See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html)

Source code:
++++++++++++

http://hgdownload.cse.ucsc.edu/admin/exe/

]]></help>
<citations>
      <citation type="doi">10.1101/gr.229202</citation>
</citations>
</tool>