<tool id="magicblast" name="Magic-BLAST: map large RNA or DNA sequences" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>against a whole genome or transcriptome</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
#import os

magicblast
-num_threads \${GALAXY_SLOTS:-8}
#if $query.is_of_type('fasta.gz', 'fastqsanger.gz'):
    -query <(gunzip -c '${query}')
#else:
    -query '${query}'
#end if
#if $query_mate:
    -paired
    #if $query.is_of_type('fasta.gz', 'fastqsanger.gz'):
        -query_mate <(gunzip -c '${query}')
    #else:
        -query_mate '${query}'
    #end if
#end if

#if $query.is_of_type('fastqsanger', 'fastqsanger.gz'):
    -infmt fastq
#end if

#if $db_opts.db_opts_selector == "histdb":
    -db '${os.path.join($db_opts.histdb.extra_files_path, "blastdb")}'
#elif $db_opts.db_opts_selector == "db":
    -db '${db_opts.database.fields.path}'
#else:
    #if $db_opts.subject.is_of_type('fasta.gz'):
        -subject <(gunzip -c '${$db_opts.subject}')
    #else:
        -subject '${db_opts.subject}'
    #end if
#end if

## General search options
-word_size $general_search.word_size
-gapopen $general_search.gapopen
-gapextend $general_search.gapextend
-penalty $general_search.penalty
-max_intron_length $general_search.max_intron_length

## Query filtering options
$query_filtering.lcase_masking
-validate_seqs $query_filtering.validate_seqs
-limit_lookup $query_filtering.limit_lookup
-max_db_word_count $query_filtering.max_db_word_count
-lookup_stride $query_filtering.lookup_stride

## Restrict database search
#if $restrict_search.gilist:
    -gilist '$restrict_search.gilist'
#end if
#if $restrict_search.negative_gilist:
    -negative_gilist '$restrict_search.negative_gilist'
#end if
#if $restrict_search.seqidlist:
    -seqidlist '$restrict_search.seqidlist'
#end if
#if $restrict_search.negative_seqidlist:
    -negative_seqidlist '$restrict_search.negative_seqidlist'
#end if
#if str($restrict_search.taxids) != '':
    --taxids '$restrict_search.taxids'
#end if
#if $restrict_search.taxidlist:
    -taxidlist '$restrict_search.taxidlist'
#end if
#if str($restrict_search.negative_taxids) != '':
    --negative_taxids '$restrict_search.negative_taxids'
#end if
#if $restrict_search.negative_taxidlist:
    -negative_taxidlist '$restrict_search.negative_taxidlist'
#end if

## Mapping options
-score $mapping.score
#if $mapping.max_edit_dist > 0:
    -max_edit_dist $mapping.max_edit_dist
#end if
-splice '$mapping.splice'
-reftype '$mapping.reftype'

## Output unaligned options
#if str($output_options.report_unaligned_cond.report_unaligned) == 'yes':
    #if str($output_options.report_unaligned_cond.report_unaligned_separately_cond.report_unaligned_separately) == 'yes':
        -out_unaligned 'out_unaligned'
        #if str($output_options.report_unaligned_cond.report_unaligned_separately_cond.unaligned_fmt_cond.unaligned_fmt) == 'bam':
            -unaligned_fmt 'sam'
        #else:
            -unaligned_fmt '$output_options.report_unaligned_cond.report_unaligned_separately_cond.unaligned_fmt_cond.unaligned_fmt'
        #end if
    #end if
#else:
    -no_unaligned
#end if

## Additional output options
$output_options.no_discordant
## Switch default SAM output to be BAM.
#if str($output_options.outfmt_cond.outfmt) == 'bam':
    $output_options.outfmt_cond.md_tag
    #if $query_mate:
        $output_options.outfmt_cond.no_query_id_trim
    #end if
    -out 'output.sam'
    #if str($output_options.outfmt_cond.output_sort) == 'coordinate':
        && samtools sort -@\${GALAXY_SLOTS:-4} -O bam 'output.sam' > '$output'
    #elif str($output_options.outfmt_cond.output_sort) == 'name':
        && samtools sort -n -@\${GALAXY_SLOTS:-4} -O bam -o 'output.sam' > '$output'
    #else:
        && samtools view -@\${GALAXY_SLOTS:-4} -bS 'output.sam' > '$output'
    #end if
#else:
    -out '$output'
    -outfmt '$output_options.outfmt_cond.outfmt'
#end if

## Convert out_unaligned from SAM to BAM if necessary

#if str($output_options.report_unaligned_cond.report_unaligned) == 'yes':
    #if str($output_options.report_unaligned_cond.report_unaligned_separately_cond.report_unaligned_separately) == 'yes':
        #if str($output_options.report_unaligned_cond.report_unaligned_separately_cond.unaligned_fmt_cond.unaligned_fmt) == 'bam':
            #if str($output_options.report_unaligned_cond.report_unaligned_separately_cond.unaligned_fmt_cond.output_sort) == 'coordinate':
                && samtools sort -@\${GALAXY_SLOTS:-4} -O bam -o 'out_unaligned' > '$output_unaligned'
            #elif str($output_options.report_unaligned_cond.report_unaligned_separately_cond.unaligned_fmt_cond.output_sort) == 'name':
                && samtools sort -n -@\${GALAXY_SLOTS:-4} -O bam -o 'out_unaligned' > '$output_unaligned'
            #else:
                && samtools view -@\${GALAXY_SLOTS:-4} -bS 'out_unaligned' > '$output_unaligned'
            #end if
        #else:
            && mv 'out_unaligned' '$output_unaligned'
        #end if
    #end if
#end if
    ]]></command>
    <inputs>
        <param argument="-query" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Query file" help="Fasta or fastqsanger, optionally gzipped"/>
        <param argument="-query_mate" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" optional="true" label="Query mate file (optional)" help="Fasta or fastqsanger, optionally gzipped"/>
        <conditional name="db_opts">
            <param name="db_opts_selector" type="select" label="Subject database/sequences">
              <option value="histdb" selected="true">blast database from your history</option>
              <option value="db">Locally installed blast database</option>
              <option value="file">fasta file from your history (see warning in the tool help section below)</option>
            </param>
            <when value="histdb">
                <param name="histdb" type="data" format="blastdbn" label="Nucleotide blast database"/>
            </when>
            <when value="db">
                <param name="database" type="select" optional="false" label="Nucleotide blast database">
                    <options from_data_table="blastdb"/>
                </param>
            </when>
            <when value="file">
                <param argument="-subject" type="data" format="fasta,fasta.gz" label="Nucleotide fasta subject file to use instead of a database"/>
            </when>
        </conditional>
        <section name="general_search" title="General search">
            <param argument="-word_size" type="integer" value="18" min="12" label="Minimum number of consecutive bases matching exactly"/>
            <param argument="-gapopen" type="integer" value="0" min="0" label="Cost to open a gap"/>
            <param argument="-gapextend" type="integer" value="0" min="0" label="Cost to extend a gap"/>
            <param argument="-penalty" type="integer" value="-4" max="0" label="Penalty for a nucleotide mismatch"/>
            <param argument="-max_intron_length" type="integer" value="500000" min="0" label="Maximum allowed intron length"/>
        </section>
        <section name="query_filtering" title="Query filtering">
            <param argument="-lcase_masking" type="boolean" truevalue="-lcase_masking" falsevalue="" checked="false" label="Use lower case filtering in subject sequences?"/>
            <param argument="-validate_seqs" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Reject low quality sequences?"/>
            <param argument="-limit_lookup" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Remove word seeds with high frequency in the searched database?"/>
            <param argument="-max_db_word_count" type="integer" value="30" min="0" label="Words that appear more than this number of times in the database will be masked in the lookup table"/>
            <param argument="-lookup_stride" type="integer" value="0" min="0" label="Number of words to skip after collecting one while creating a lookup table"/>
        </section>
        <section name="restrict_search" title="Restrict database search">
            <param argument="-gilist" type="data" format="tabular" optional="true" label="Tabular file containing list of GIs to which to restrict database search" help="Available only for database searches"/>
            <param argument="-negative_gilist" type="data" format="tabular" optional="true" label="Tabular file containing list of GIs to restrict database search to everything except the specified GIs" help="Available only for database searches"/>
            <param argument="-seqidlist" type="data" format="tabular" optional="true" label="Tabular file containing list of SeqIDs to which to restrict database search" help="Available only for database searches"/>
            <param argument="-negative_seqidlist" type="data" format="tabular" optional="true" label="Tabular file containing list of SeqIDs to restrict database search to everything except the specified SeqIDs" help="Available only for database searches"/>
            <param argument="-taxids" type="text" optional="true" label="Comma-separated list of taxonomy IDs to which to restrict database search" help="Available only for database searches">
                <expand macro="sanitize_query" validinitial="string.ascii_letters,string.digits,string.whitespace,string.punctuation"/>
            </param>
            <param argument="-taxidlist" type="data" format="tabular" optional="true" label="Tabular file containing list of taxonomy IDs to which to restrict database search" help="Available only for database searches"/>
            <param argument="-negative_taxids" type="text" optional="true" label="Comma-separated list of taxonomy IDs to restrict database search to everything except the specified taxonomy IDs" help="Available only for database searches">
                <expand macro="sanitize_query" validinitial="string.ascii_letters,string.digits,string.whitespace,string.punctuation"/>
            </param>
            <param argument="-negative_taxidlist" type="data" format="tabular" optional="true" label="Tabular file containing list of taxonomy IDs to restrict database search to everythin except the specified taxonomy IDs" help="Available only for database searches"/>
        </section>
        <section name="mapping" title="Mapping">
            <param argument="-score" type="integer" value="0" min="0" label="Cutoff score for accepting alignments" help="Zero value ignores"/>
            <param argument="-max_edit_dist" type="integer" value="0" min="0" label="Cutoff edit distance for accepting an alignment" help="Zero value is unlimited"/>
            <param argument="-splice" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Search for spliced alignments?"/>
            <param argument="-reftype" type="select" label="Type of the reference">
                <option value="genome" selected="true">genome</option>
                <option value="transcriptome">transcriptome</option>
            </param>
        </section>
        <section name="output_options" title="Output options">
            <conditional name="report_unaligned_cond">
                <param name="report_unaligned" type="select" label="Report unaligned reads?">
                    <option value="yes" selected="true">Yes</option>
                    <option value="no">No</option>
                </param>
                <when value="yes">
                    <conditional name="report_unaligned_separately_cond">
                        <param name="report_unaligned_separately" type="select" label="Output unaligned reads to a separate file?" help="Select No to output all reads to the same file">
                            <option value="no" selected="true">No</option>
                            <option value="yes">Yes</option>
                        </param>
                        <when value="no"/>
                        <when value="yes">
                            <conditional name="unaligned_fmt_cond">
                                <param argument="-unaligned_fmt" type="select" label="Output format for unaligned reads">
                                    <option value="bam" selected="true">bam</option>
                                    <option value="tabular">tabular</option>
                                    <option value="fasta">fasta</option>
                                </param>
                                <when value="bam">
                                    <expand macro="output_sort_param"/>
                                </when>
                                <when value="tabular"/>
                                <when value="fasta"/>
                            </conditional>
                        </when>
                    </conditional>
                </when>
                <when value="no"/>
            </conditional>
            <conditional name="outfmt_cond">
                <param argument="-outfmt" type="select" label="Output format">
                    <option value="bam" selected="true">bam</option>
                    <option value="tabular">tabular</option>
                </param>
                <when value="bam">
                    <expand macro="output_sort_param"/>
                    <param argument="-md_tag" type="boolean" truevalue="-md_tag" falsevalue="" checked="false" label="Include MD tag in BAM output?"/>
                    <param argument="-no_query_id_trim" type="boolean" truevalue="-no_query_id_trim" falsevalue="" checked="false" label="Do not trim '.1', '/1', '.2', or '/2' at the end of read ids in BAM output for paired reads?" help="Ignored if no query mate"/>
                </when>
                <when value="tabular"/>
            </conditional>
            <param argument="-no_discordant" type="boolean" truevalue="-no_discordant" falsevalue="" checked="false" label="Suppress discordant alignments for paired reads?" help="Ignored if no query mate"/>
        </section>
    </inputs>
    <outputs>
        <data name="output" format="bam" label="${tool.name} on ${on_string}">
            <change_format>
                <when input="output_options.outfmt_cond.outfmt" value="tabular" format="tabular"/>
            </change_format>
        </data>
        <data name="output_unaligned" format="bam" label="${tool.name} on ${on_string}: unaligned reads">
            <filter>output_options['report_unaligned_cond']['report_unaligned'] == 'yes' and output_options['report_unaligned_cond']['report_unaligned_separately_cond']['report_unaligned_separately'] == 'yes'</filter>
            <change_format>
                <when input="output_options.report_unaligned_cond.report_unaligned_separately_cond.unaligned_fmt_cond.unaligned_fmt" value="tabular" format="tabular"/>
                <when input="output_options.report_unaligned_cond.report_unaligned_separately_cond.unaligned_fmt_cond.unaligned_fmt" value="fasta" format="fasta"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <!-- Single fasta.gz input, subject file -->
        <test expect_num_outputs="1">
            <param name="query" value="query1.fasta.gz" ftype="fasta.gz"/>
            <param name="db_opts_selector" value="file"/>
            <param name="subject" value="subject1.fasta.gz" ftype="fasta.gz"/>
            <output name="output" ftype="bam">
                <assert_contents>
                    <has_size value="1247" delta="50"/>
                </assert_contents>
            </output>
        </test>
        <!-- Single fasta.gz input, subject file, output unaligned reads separately-->
        <test expect_num_outputs="2">
            <param name="query" value="query1.fasta.gz" ftype="fasta.gz"/>
            <param name="db_opts_selector" value="file"/>
            <param name="subject" value="subject1.fasta.gz" ftype="fasta.gz"/>
            <param name="report_unaligned_separately" value="yes"/>
            <param name="unaligned_fmt" value="tabular"/>
            <output name="output" ftype="bam">
                <assert_contents>
                    <has_size value="492" delta="50"/>
                </assert_contents>
            </output>
            <output name="output_unaligned" ftype="tabular">
                <assert_contents>
                    <has_size value="959"/>
                </assert_contents>
            </output>
        </test>
        <!-- Single fasta.gz input, subject file, gilist file, results in error -->
        <test expect_failure="true">
            <param name="query" value="query1.fasta.gz" ftype="fasta.gz"/>
            <param name="db_opts_selector" value="file"/>
            <param name="subject" value="subject1.fasta.gz" ftype="fasta.gz"/>
            <param name="report_unaligned_separately" value="yes"/>
            <param name="gilist" value="gilist1.tabular" ftype="tabular"/>
            <assert_stderr>
                <has_text text="Incompatible with argument:"/>
            </assert_stderr>
        </test>
        <!-- Single fasta.gz input, cached db, taxidlist, results in error -->
        <test expect_failure="true">
            <param name="query" value="query1.fasta.gz" ftype="fasta.gz"/>
            <param name="db_opts_selector" value="db"/>
            <param name="database" value="phiX174"/>
            <param name="taxidlist" value="taxids.tabular" ftype="tabular"/>
            <assert_stderr>
                <has_text text="Taxonomy filtering is not supported in v4 BLAST dbs"/>
            </assert_stderr>
        </test>
        <!-- Paired fastqsanger.gz input, subject file -->
        <test expect_num_outputs="1">
            <param name="query" value="query_forward1.fastqsanger.gz" ftype="fastqsanger.gz"/>
            <param name="query_mate" value="query_reverse1.fastqsanger.gz" ftype="fastqsanger.gz"/>
            <param name="db_opts_selector" value="file"/>
            <param name="subject" value="subject1.fasta.gz" ftype="fasta.gz"/>
            <output name="output" ftype="bam">
                <assert_contents>
                    <has_size value="61454" delta="50"/>
                </assert_contents>
            </output>
        </test>
        <!-- Paired fastqsanger.gz input, cached blast db -->
        <test expect_num_outputs="1">
            <param name="query" value="query_forward1.fastqsanger.gz" ftype="fastqsanger.gz"/>
            <param name="query_mate" value="query_reverse1.fastqsanger.gz" ftype="fastqsanger.gz"/>
            <param name="db_opts_selector" value="db"/>
            <param name="database" value="phiX174"/>
            <output name="output" ftype="bam">
                <assert_contents>
                    <has_size value="61457" delta="50"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

.. class:: warningmark

In addition to a BLAST database, you can also search against a fasta file of subject (target) sequences. However, this is not
advised because it is slower (only one CPU is used), but more importantly gives e-values for pairwise searches (very small
e-values which will look overly signficiant).  In most cases you should convert the fasta file into a blast database using
*makeblastdb* and search against that.

Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.
Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq,
locating the candidate introns and adding up the score of all exons. This is very different from other versions of BLAST, where
each exon is scored as a separate hit and read-pairing is ignored.

Magic-BLAST incorporates within the NCBI BLAST code framework ideas developed in the NCBI Magic pipeline, in particular hit
extensions by local walk and jump, and recursive clipping of mismatches near the edges of the reads, which avoids accumulating
artefactual mismatches near splice sites and is needed to distinguish short indels from substitutions near the edges.

The tool accepts a single or paired set of reads in fasta or fastqsanger format and produces bam or tabular output.

More information about Magic-BLAST is available in the
`online documentation <https://ncbi.github.io/magicblast/>`_.
    ]]></help>
    <expand macro="citations"/>
</tool>