<tool id="data_manager_malt_index_builder" name="MALT index builder" tool_type="manage_data" version="@TOOL_VERSION@+galaxy0" profile="21.01">
    <description></description>
    <requirements>
        <requirement type="package" version="3.8">python</requirement>
        <requirement type="package" version="0.53">malt</requirement>
    </requirements>
    <macros>
        <token name="@TOOL_VERSION@">0.5.3</token>
    </macros>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/malt_index_builder.py'
'${out_file}'
--fasta_filename '${all_fasta_source.fields.path}'
--fasta_dbkey '${all_fasta_source.fields.dbkey}'
--fasta_description '${all_fasta_source.fields.name}'
--sequence_type '${sequence_type}'
#if str($protein_reduct_setting_cond.protein_reduct_setting) == 'yes':
    --protein_reduct '${protein_reduct_setting_cond.protein_reduct}'
#end if
#if str($seed_setting_cond.seed_setting) == 'yes':
    --shapes '${seed_setting_cond.shapes}'
    ## malt-build requires a string here.
    --max_hits_per_seed '${seed_setting_cond.max_hits_per_seed}'
#end if
    ]]></command>
    <inputs>
        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
            <options from_data_table="all_fasta"/>
        </param>
        <param name="sequence_name" type="text" value="" label="Name of sequence"/>
        <param name="sequence_id" type="text" value="" label="ID for sequence"/>
        <param  name="sequence_type" type="select" label="Reference sequences type" help="Use the DNA setting For RNA sequences">
            <option value="DNA" selected="true">DNA</option>
            <option value="Protein">Protein</option>
        </param>
        <conditional name="protein_reduct_setting_cond">
            <param name="protein_reduct_setting" type="select" label="Specify protein alphabet reduction?" help="Used only if the reference sequences are Protein sequences">
                <option selected="true" value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <param name="protein_reduct" type="select" label="Name or definition of protein alphabet reduction">
                    <option selected="true" value="DIAMOND_11">DIAMOND_11</option>
                    <option value="BLOSUM50_10">BLOSUM50_10</option>
                    <option value="BLOSUM50_11">BLOSUM50_11</option>
                    <option value="BLOSUM50_15">BLOSUM50_15</option>
                    <option value="BLOSUM50_4">BLOSUM50_4</option>
                    <option value="BLOSUM50_8">BLOSUM50_8</option>
                    <option value="GBMR4">GBMR4</option>
                    <option value="HSDM17">HSDM17</option>
                    <option value="MALT_10">MALT_10</option>
                    <option value="SDM12">SDM12</option>
                    <option value="UNREDUCED">UNREDUCED</option>
                </param>
            </when>
        </conditional>
        <conditional name="seed_setting_cond">
            <param name="seed_setting" type="select" label="Specify seed settings?">
                <option selected="true" value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <param name="shapes" type="text" value="" label="Comma-separated list of seed shapes" help="See help text below">
                    <sanitizer invalid_char="">
                        <valid initial="string.printable">
                            <remove value="&apos;"/>
                        </valid>
                        <mapping initial="none">
                            <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
                        </mapping>
                    </sanitizer>
                </param>
                <param name="max_hits_per_seed" type="integer" value="1" min="1" label="Maximum number of hits per seed"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <param name="all_fasta_source" value="phiX174"/>
            <param name="sequence_name" value="Pretty name for phiX174"/>
            <param name="sequence_id" value="phiX174-1"/>
            <output name="out_file" value="malt_index_builder1.json"/>
        </test>
        <test>
            <param name="all_fasta_source" value="phiX174"/>
            <param name="sequence_name" value="Pretty name for phiX174"/>
            <param name="sequence_id" value="phiX174-1"/>
            <param name="seed_setting" value="yes"/>
            <param name="shapes" value="111110111011110110111111"/>
            <output name="out_file" value="malt_index_builder1.json"/>
        </test>
        <test>
            <param name="all_fasta_source" value="phiX174"/>
            <param name="sequence_name" value="Pretty name for phiX174"/>
            <param name="sequence_id" value="phiX174-2"/>
            <param name="sequence_type" value="Protein"/>
            <param name="protein_reduct_setting" value="yes"/>
            <param name="protein_reduct" value="BLOSUM50_10"/>
            <output name="out_file" value="malt_index_builder2.json"/>
        </test>
    </tests>
    <help>
.. class:: infomark

**Notice:** Values for Name and ID of sequence will be generated automatically if left blank.

**What it does**

Takes a reference sequence database (represented by a FastA file, possibly in gzip format) as input and produces an index that
can be used by the malt tool as input. If MALT is to be used as a taxonomic and/or functional analysis tool as well as an
alignment tool, then this MALT index builder tool must be provided with a number of mapping files that are used to map reference
sequences to taxonomic or functional classes or to locate genes in DNA reference sequences.

**Options**

 * **Specify protein alphabet reduction** - specify the alphabet reduction in the case of protein reference sequences.
 * **Specify seed settings** - specify the settings for controlling how MALT uses its seed-and-extend approach based on “spaced seeds”.

  * **Shapes** - specify the seed shapes used. For DNA sequences, the default seed shape is: 111110111011110110111111. For protein sequences, by default MALT uses the following four shapes: 111101101110111, 1111000101011001111, 11101001001000100101111 and 11101001000010100010100111.
  * **Maximim hits per seed** - specify the maximum number of hits per seed - MALT uses this to calculate a maximum number of hits per hash value.

    </help>
    <citations>
        <citation type="doi">https://doi.org/10.1101/050559</citation>
    </citations>
</tool>