<tool id="bg_diamond_view" name="Diamond view" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
    <description>generate formatted output from DAA files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command detect_errors="aggressive"><![CDATA[
    ## need to link because diamont tries to open dataset_xxx.dat.daa
    ln -s '$daa' input.daa &&
    diamond
        view
        --threads \${GALAXY_SLOTS:-1}
        --daa input.daa
        @OUTPUT_ARGS@
        @HITFILTER_ARGS@
        $forwardonly
        --compress '0'
    ]]>
    </command>
    <inputs>
        <param argument="--daa" type="data" format="daa" label="input file in DAA format" />
        <section name="output_section" title="Output options">
            <expand macro="output_type_macro" />
        </section>
        <expand macro="hit_filter_macro" />
        <param argument="--forwardonly" type="boolean" truevalue="--forwardonly" falsevalue="" checked="false" label="only show alignments of forward strand" help=""/>
    </inputs>
    <outputs>
        <expand macro="output_macro" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="daa" ftype="daa" value="diamond_results.daa" />
            <section name="output_section">
                <conditional name="output">
                    <param name="outfmt" value="5"/>
                </conditional>
            </section>
            <conditional name="hit_filter">
                <param name="hit_filter_select" value="max"/>
                <param name="max_target_seqs" value="1" />
            </conditional>
            <output name="blast_tabular" file="diamond_results.xml"/>
        </test>
        <test expect_num_outputs="1">
            <param name="daa" ftype="daa" value="diamond_results.daa" />
            <section name="output_section">
                <conditional name="output">
                    <param name="outfmt" value="6"/>
                    <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,cigar,scovhsp"/>
                </conditional>
            </section>
            <output name="blast_tabular" file="diamond_view_results.tabular"/>
        </test>
        <test expect_num_outputs="1">
            <param name="daa" ftype="daa" value="diamond_results.daa" />
            <section name="output_section">
                <conditional name="output">
                    <param name="outfmt" value="101"/>
                </conditional>
            </section>
            <conditional name="hit_filter">
                <param name="hit_filter_select" value="top"/>
                <param name="max_target_seqs" value="1" />
            </conditional>
            <param name="forwardonly" value="--forwardonly" />
            <output name="blast_tabular" file="diamond_results.sam" lines_diff="2"/>
        </test>
    </tests>

    <help>
<![CDATA[

**What it does**

Converts diamond daa files to multiple other formats.

**Input**

Input data is a daa file.


**Output**

Alignment results in BLAST format (pairwise/tabular), xml, sam, taxonomic (Note the latter does not work with the current diamond version. )

BLAST tables contain the following columns.

Column 	Description
1 	    Query Seq-id (ID of your sequence)
2 	    Subject Seq-id (ID of the database hit)
3 	    Percentage of identical matches
4 	    Alignment length
5 	    Number of mismatches
6 	    Number of gap openings
7 	    Start of alignment in query
8 	    End of alignment in query
9 	    Start of alignment in subject (database hit)
10 	    End of alignment in subject (database hit)
11 	    Expectation value (E-value)
12 	    Bit score
]]>
    </help>
    <expand macro="citations" />
</tool>