<tool id="qiime_filter_fasta" name="Filter fasta" version="@WRAPPER_VERSION@.0" profile="@PROFILE@">
    <description>to remove sequences based on input criteria (filter_fasta)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
@MPLBACKEND@
filter_fasta.py
    --input_fasta_fp '$input_fasta_fp'
    --output_fasta_fp '$fitered_fasta'
    #if $selection.type == "otu_map"
        --otu_map '$selection.otu_map'
    #else if $selection.type == "seq_list"
        --seq_id_fp '$selection.seq_id_fp'
    #else if $selection.type == "biom"
        --biom_fp '$selection.biom_fp'
    #else if $selection.type == "fasta"
        --subject_fasta_fp '$selection.subject_fasta_fp'
    #else if $selection.type == "prefix"
        --seq_id_prefix '$selection.seq_id_prefix'
    #else if $selection.type == "prefix_list"
        --sample_id_fp '$selection.sample_id_fp'
    #else if $selection.type == "valid_states"
        --mapping_fp '$selection.mapping_fp'
        --valid_states '$selection.valid_states'
    #end if
    $negate
    ]]></command>
    <inputs>
        <param name="input_fasta_fp" argument="--input_fasta_fp" type="data" format="fasta" label="Input fasta file"/>
        <conditional name="selection">
            <param name="type" label="Type of criteria for filtering" type="select">
                <option value="otu_map">OTU map-based filtering</option>
                <option value="seq_list">Filtering using a list of sequence identifiers</option>
                <option value="biom">Filtering based on OTU identifiers in a BIOM file</option>
                <option value="fasta">Filtering based on sequence identifiers in a Fasta file</option>
                <option value="prefix">Filtering based on a sequence id prefix</option>
                <option value="prefix_list">Filtering based on a list of sequence id prefix</option>
                <option value="valid_states">Filtering based on a sample id description</option>
            </param>
            <when value="otu_map">
                <param argument="--otu_map" type="data" format="txt" label="OTU map where sequences ids are those which should be retained"/>
            </when>
            <when value="seq_list">
                <param argument="--seq_id_fp" type="data" format="tabular,tsv,csv,txt" label="List of sequence identifiers (or tab-delimited lines with a seq identifier in the first field) which should be retained"/>
            </when>
            <when value="biom">
                <param argument="--biom_fp" type="data" format="biom1" label="Biom file with OTU identifiers that should be retained"/>
            </when>
            <when value="fasta">
                <param argument="--subject_fasta_fp" type="data" format="fasta" label="Fasta file where the seq ids should be retained"/>
            </when>
            <when value="prefix">
                <param argument="--seq_id_prefix" type="text" label="Prefix to keep seqs where seq_id starts with this prefix"/>
            </when>
            <when value="prefix_list">
                <param argument="--sample_id_fp" type="data" format="txt" label="List of prefix to keep seqs where seq_id starts with a sample id listed in this file"/>
            </when>
            <when value="valid_states">
                <param argument="--mapping_fp" type="data" format="txt" label="Mapping file"/>
                <param argument="--valid_states" type="text" label="Description of the sample ids to retain"/>
            </when>
        </conditional>
        <param argument="--negate" type="boolean" truevalue="--negate" falsevalue="" checked="false" label="Discard passed seq ids rather than keep passed seq ids?"/>        
    </inputs>
    <outputs>
        <data name="fitered_fasta" format="fasta" label="${tool.name} on ${on_string}: Filtered sequences"/>
    </outputs>
    <tests>
        <test>
            <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/>
            <param name="type" value="otu_map"/>
            <param name="otu_map" value="filter_fasta/otu_map.txt"/>
            <param name="negate" value=""/>
            <output name="fitered_fasta" md5="9185f3cdcba8bcaf159cc3f1fdbb5ebb"/>
        </test>
        <test>
            <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/>
            <param name="type" value="otu_map"/>
            <param name="otu_map" value="filter_fasta/otu_map.txt"/>
            <param name="negate" value="--negate"/>
            <output name="fitered_fasta" md5="206a5c83e5abbd674f632da73ec518a2"/>
        </test>
        <test>
            <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/>
            <param name="type" value="seq_list"/>
            <param name="seq_id_fp" value="filter_fasta/seqs_to_keep.txt"/>
            <param name="negate" value=""/>
            <output name="fitered_fasta" md5="19ba95928ca9419f671810240120c8cd"/>
        </test>
        <test>
            <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/>
            <param name="type" value="biom"/>
            <param name="biom_fp" value="filter_fasta/otu_table.biom"/>
            <param name="negate" value=""/>
            <output name="fitered_fasta" md5="d41d8cd98f00b204e9800998ecf8427e"/>
        </test>
        <test>
            <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/>
            <param name="type" value="fasta"/>
            <param name="subject_fasta_fp" value="filter_fasta/sl_inseqs.fasta"/>
            <param name="negate" value=""/>
            <output name="fitered_fasta" md5="9c5f416e94bcfb2d4003ea002cbaf617"/>
        </test>
        <test>
            <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/>
            <param name="type" value="prefix"/>
            <param name="seq_id_prefix" value="S5"/>
            <param name="negate" value=""/>
            <output name="fitered_fasta" md5="c1f2d8c5844733f30ca07547846c4d36"/>
        </test>
        <test>
            <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/>
            <param name="type" value="prefix_list"/>
            <param name="sample_id_fp" value="filter_fasta/map.txt"/>
            <param name="negate" value=""/>
            <output name="fitered_fasta" md5="8f0025b067d22ed708ee55de10016785"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Filter fasta or fastq file to remove sequences based on input criteria
    ]]></help>
    <citations>
        <expand macro="citations"/>
    </citations>
</tool>