<tool id="mycrobiota-qc-report" name="QC report" version="1">
    <description>from count tables</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <command detect_errors="aggressive"><![CDATA[
        python '$__tool_directory__/mycrobiota.py'
            --command qc_report
            #if $input.filetype == 'summarylog':
                #for $i, $c in enumerate($input.summaryfiles):
                    --summary_log '${c.summary}'
                    --label '${c.label}'
                #end for
            #elif $input.filetype == 'counttable':
                #for $i, $c in enumerate($input.counttables):
                    --count_table '${c.count_table}'
                    --label '${c.label}'
                #end for
            #end if
    ]]></command>
    <inputs>
        <conditional name="input">
            <param name="filetype" type="select" label="Generate QC table from" help="">
                <option value="counttable">count tables</option>
                <option value="summarylog">summary.seqs log outputs</option>
            </param>
            <when value="counttable">
                <repeat name="counttables" title="Count Table" default="1" >
                    <param argument="--count_table" type="data" format="mothur.count_table" label="Coumt Table" help=""/>
                    <param argument="--label" type="text" size="100" value="" label="Enter a label for this step" help="e.g. trimmed by length"/>
                </repeat>
            </when>
            <when value="summarylog">
                <repeat name="summaryfiles" title="Summary.seqs output log" default="1" >
                    <param argument="--summary" type="data" format="text" label="Summary File" help="logfile output of summary.seqs command"/>
                    <param argument="--label" type="text" size="100" value="" label="Enter a label for this step" help="e.g. trimmed by length"/>
                </repeat>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="allsamples" format="tabular" from_work_dir="all_qctable.tsv" label="${tool.name} on ${on_string}: QC table total counts"/>
        <collection name="persample" type="list" label="${tool.name} on ${on_string}: per-sample QC tables">
            <discover_datasets pattern=".*?persample_qctable_(?P&lt;designation&gt;.*)\.tsv" format="tabular"/>
            <filter> input['filetype'] == 'counttable' </filter>
        </collection>
    </outputs>
    <tests>
        <test><!-- test with count tables -->
            <param name="filetype" value="counttable"/>
            <repeat name="counttables">
                <param name="count_table" value="test2.count_table"/>
                <param name="label" value="step1"/>
            </repeat>
            <repeat name="counttables">
                <param name="count_table" value="test.count_table"/>
                <param name="label" value="step2"/>
            </repeat>
            <output name="allsamples" md5="97725d04b9927724729f6cd902e10317" ftype="tabular"/>
            <output_collection name="persample" count="9">
                <element name="F3D144" md5="d86e633358e8f1518a4a8c2782a358ec"/>
            </output_collection>
        </test>
        <test><!-- test with summary logfiles -->
            <param name="filetype" value="summarylog"/>
            <repeat name="summaryfiles">
                <param name="summary" value="summarylog1.txt"/>
                <param name="label" value="step1"/>
            </repeat>
            <repeat name="summaryfiles">
                <param name="summary" value="summarylog2.txt"/>
                <param name="label" value="step2"/>
            </repeat>
            <repeat name="summaryfiles">
                <param name="summary" value="summarylog3.txt"/>
                <param name="label" value="step 3"/>
            </repeat>
            <output name="allsamples" md5="7e092deb126c537247e63a36def1d8fb" ftype="tabular"/>
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Given a set of count tables, make a summary table describing the differences in number of sequences.
]]>
    </help>
    <expand macro="citations"/>
</tool>