<tool id="qiime_filter_fasta" name="filter fasta" version="1.9.1galaxy1">
    <description>This script can be applied to remove sequences from a fasta or 
        fastq file based on input criteria.</description>

    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements" />

    <command>
<![CDATA[        
        filter_fasta.py 
            -f $input_fasta_fp 
            -o $output_fasta_fp
            #if str($otu_map) != 'None':
             -m $otu_map
            #end if

            #if str($seq_id_fp) != 'None':
             -s $seq_id_fp
            #end if

            #if str($biom_fp) != 'None':
             -b $biom_fp
            #end if

            #if str($subject_fasta_fp) != 'None':
             -a $subject_fasta_fp
            #end if

            #if str($seq_id_prefix):
             -p $seq_id_prefix
            #end if

            #if str($sample_id_fp) != 'None':
             --sample_id_fp=$sample_id_fp
            #end if

            #if $negate:
             -n
            #end if

            #if str($mapping_fp) != 'None':
             --mapping_fp=$mapping_fp
            #end if

            #if str($valid_states):
             --valid_states=$valid_states
            #end if
]]>
    </command>

    <inputs>
        <param label="-f/--input_fasta_fp: path to the input fasta file" 
            name="input_fasta_fp" optional="False" type="data"/>
        <param label="-m/--otu_map: an OTU map where sequences ids are those 
            which should be retained" name="otu_map" optional="True" type="data"/>
        <param label="-s/--seq_id_fp: A list of sequence identifiers (or tab-delimited 
            lines with a seq identifier in the first field) which should be retained" 
            name="seq_id_fp" optional="True" type="data"/>
        <param label="-b/--biom_fp: A biom file where otu identifiers should be 
            retained" name="biom_fp" optional="True" type="data"/>
        <param label="-a/--subject_fasta_fp: A fasta file where the seq ids should 
            be retained." name="subject_fasta_fp" optional="True" type="data"/>
        <param label="-p/--seq_id_prefix: keep seqs where seq_id starts with this 
            prefix" name="seq_id_prefix" optional="True" type="text"/>
        <param label="--sample_id_fp: keep seqs where seq_id starts with a sample 
            id listed in this file" name="sample_id_fp" optional="True" 
            type="data"/>
        <param label="-n/--negate: discard passed seq ids rather than keep passed 
            seq ids [default: False]" name="negate" selected="False" 
            type="boolean"/>
        <param label="--mapping_fp: mapping file path (for use with --valid_states) 
            [default: None]" name="mapping_fp" optional="True" type="data"/>
        <param label="--valid_states: description of sample ids to retain (for use 
            with --mapping_fp) [default: None]" name="valid_states" optional="True" 
            type="text"/>
    </inputs>

    <outputs>
        <data format="txt" name="output_fasta_fp"/>
    </outputs>

    <tests>
        <test>
        </test>
    </tests>

    <help>
<![CDATA[

**What it does**


    ]]>
    </help>

    <citations>
        <expand macro="citations" />
    </citations>
</tool>