<tool profile="16.07" id="mothur_sffinfo" name="Sffinfo" version="@WRAPPER_VERSION@.0">
    <description>Summarize the quality of sequences</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 "$sff" sff.dat &&
        ln -s "$accnos" accnos.dat &&
        #if $oligo.add == "yes":
            ln -s "$oligo.oligos" oligo.oligos.dat &&
        #end if

        echo 'sffinfo(
            sff=sff.dat,
            fasta=$fasta,
            qfile=$qfile,
            $sfftxt
            flow=$flow,
            trim=$trim
            #if $accnos:
                ,accnos=accnos.dat
            #end if
            #if $oligo.add == "yes":
                ,oligos=oligo.oligos.dat
                ,bdiffs=$oligo.bdiffs
                ,pdiffs=$oligo.pdiffs
                ,tdiffs=$oligo.tdiffs
                ,ldiffs=$oligo.ldiffs
                ,sdiffs=$oligo.sdiffs
            #end if
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="sff" type="data" format="sff" label="sff - Sff data"/>
        <conditional name="oligo">
            <param name="add" type="select" label="Trim with an oligos file?" help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words &quot;forward&quot;, &quot;reverse&quot;, and &quot;barcode&quot; or it can start with a &quot;#&quot; to tell mothur to ignore that line of the oligos file.">
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <param name="oligos" type="data" format="mothur.oligos" label="oligos - barcodes and primers"/>
                <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (default 0)"/>
                <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/>
                <param name="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (default 0)"/>
                <param name="ldiffs" type="integer" value="0" min="0" label="ldiffs - total number of differences to allow in linker sequence (default 0)"/>
                <param name="sdiffs" type="integer" value="0" min="0" label="sdiffs - total number of differences to allow in spacer sequence (default 0)"/>
            </when>
        </conditional>
        <param name="fasta" type="boolean" truevalue="true" falsevalue="false" checked="true" label="fasta - Add fasta to your history"/>
        <param name="qfile" type="boolean" truevalue="true" falsevalue="false" checked="true" label="qfile - Add qfile to your history"/>
        <param name="sfftxt" type="boolean" truevalue="sfftxt=true," falsevalue="" checked="false" label="sfftxt - Add sfftxt to your history"/>
        <param name="flow" type="boolean" truevalue="true" falsevalue="false" checked="true" label="flow - Add flow to your history"/>
        <param name="trim" type="boolean" truevalue="true" falsevalue="false" checked="true" label="trim - Trim sequences and quality scores"/>
        <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - Limit output to named Accessions"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="out_fasta" format="fasta" from_work_dir="sff*.fasta" label="${tool.name} on ${on_string}: fasta">
            <filter>fasta</filter>
        </data>
        <data name="out_qfile" format="qual454" from_work_dir="sff*.qual" label="${tool.name} on ${on_string}: qual">
            <filter>qfile</filter>
        </data>
        <data name="out_sfftxt" format="txt" from_work_dir="sff*.sff.txt" label="${tool.name} on ${on_string}: sff.txt">
            <filter>sfftxt</filter>
        </data>
        <data name="out_flow" format="mothur.sff.flow" from_work_dir="sff*.flow" label="${tool.name} on ${on_string}: flowgram">
            <filter>flow</filter>
        </data>
        <data name="out_scrap" format="sff" from_work_dir="sff*.scrap.sff" label="${tool.name} on ${on_string}: scrap.sff">
            <filter>oligo['add'] == 'yes'</filter>
        </data>
    </outputs>
    <tests>
        <test><!-- test without oligos -->
            <param name="sff" value="Fasting_Example1.sff"/>
            <param name="sfftxt" value="true"/>
            <output name="out_fasta" md5="fbe6f4d51959d4723a8417636476d0e0" ftype="fasta"/>
            <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/>
            <output name="out_sfftxt" md5="fdc80c8e476016632d317cfd7893713c" ftype="txt"/>
            <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with oligos file -->
            <param name="sff" value="Fasting_Example1.sff"/>
            <param name="add" value="yes"/>
            <param name="oligos" value="GQY1XT001.oligos"/>
            <output name="out_fasta" md5="212fa15e1ed077cecb65ee87f17ef2e1" ftype="fasta"/>
            <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/>
            <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/>
            <output name="out_scrap" md5="f03c422fe364815e7214ad31ad135aca" ftype="sff"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The sffinfo_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.


.. _sffinfo: https://www.mothur.org/wiki/Sffinfo
]]>
    </help>
    <expand macro="citations"/>
</tool>