<tool id="qiime_make_otu_table" name="make otu table" version="1.9.1galaxy1">

    <description>Make OTU table</description>

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

    <expand macro="requirements" />
    
    <command>
<![CDATA[
        make_otu_table.py 
            -i $otu_map_fp 
            -o $output_biom_fp
            #if str($taxonomy) != 'None':
             -t $taxonomy
            #end if

            #if str($exclude_otus_fp) != 'None':
             -e $exclude_otus_fp
            #end if
]]>
    </command>

    <inputs>
        <param label="-i/--otu_map_fp: path to the input OTU map (i.e., the output 
            from pick_otus.py)" name="otu_map_fp" optional="False" type="data"/>
        <param label="-t/--taxonomy: Path to taxonomy assignment, containing the 
            assignments of taxons to sequences (i.e., resulting txt file from 
            assign_taxonomy.py) [default: None]" name="taxonomy" optional="True" 
            type="data"/>
        <param label="-e/--exclude_otus_fp: path to a file listing OTU identifiers 
            that should not be included in the OTU table (e.g., the output of 
            identify_chimeric_seqs.py) or a fasta file where seq ids should be 
            excluded (e.g., failures fasta file from align_seqs.py)" 
            name="exclude_otus_fp" optional="True" type="data"/>
    </inputs>

    <outputs>
        <data format="txt" name="output_biom_fp" label="otu_table.biom"/>
    </outputs>

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

    <help><![CDATA[

**What it does**

The script make_otu_table.py tabulates the number of times an OTU is found in each 
sample, and adds the taxonomic predictions for each OTU in the last column if a 
taxonomy file is supplied.
The output of make_otu_table.py is a biom file, where the columns correspond to 
Samples and rows correspond to OTUs and the number of times a sample appears in 
a particular OTU.
    ]]>
    </help>

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