<tool profile="16.07" id="mothur_align_check" name="Align.check" version="@WRAPPER_VERSION@.0">
    <description>Calculate the number of potentially misaligned bases</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@SHELL_OPTIONS@

## create symlinks to input datasets
ln -s '$fasta' fasta.dat &&
ln -s '$name' name.dat &&
ln -s '$count' count.dat &&
ln -s '$map' map.dat &&

echo 'align.check(
    fasta=fasta.dat,
    #if $name:
        name=name.dat,
    #end if
    #if $count:
        count=count.dat,
    #end if
    map=map.dat
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
&& cat fasta.align.check
    ]]></command>
    <inputs>
        <param argument="fasta" type="data" format="mothur.align" label="fasta - Aligned Sequences"/>
        <conditional name="ss">
            <param name="source" label="Select Secondary Structure Map from" type="select">
                <option value="cached">Cached Secondary Structure Maps</option>
                <option value="history">Your History</option>
            </param>
            <when value="cached">
                <param argument="map" type="select" label="Secondary structure map">
                    <options from_data_table="mothur_map"/>
                </param>
            </when>
            <when value="history">
                <param argument="map" format="mothur.map" type="data" label="Secondary Structure Map"/>
            </when>
        </conditional>
        <param argument="count" type="data" format="mothur.count_table" optional="true" label="count_table file"
            help="You can also provide a name file associated with your fasta file"/>
        <param argument="name" type="data" format="mothur.names" optional="true" label="names file"
            help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="align.check" format="mothur.align.check" from_work_dir="fasta.align.check" label="${tool.name} on ${on_string}: align.check"/>
    </outputs>
    <tests>
        <test><!-- test with defaults -->
            <param name="fasta" value="amazon.align_head_short"/>
            <param name="source" value="history"/>
            <param name="map" value="silva.ss.map.head"/>
            <output name="align.check" ftype="mothur.align.check">
                <assert_contents>
                    <expand macro="test-aligncheck-format"/>
                    <has_text text="U68589"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with names file -->
            <param name="fasta" value="amazon.align_head_short"/>
            <param name="source" value="history"/>
            <param name="map" value="silva.ss.map.head"/>
            <param name="name" value="amazon.align_head.names"/>
            <output name="align.check" ftype="mothur.align.check">
                <assert_contents>
                    <expand macro="test-aligncheck-format"/>
                    <has_text text="U68589"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The align.check_ command allows you to calculate the number of potentially misaligned bases in a 16S rRNA gene sequence
alignment using a secondary_structure_map_.  If you are familiar with the editor window in ARB, this is the same as
counting the number of ~, #, -, and = signs.

.. _secondary_structure_map: https://www.mothur.org/wiki/Secondary_structure_map
.. _align.check: https://www.mothur.org/wiki/Align.check

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