annotate merge.sfffiles.xml @ 7:b296d6f25ee3 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ff56a4c9218ddea84ff5cd72fd98c62db212465d"

<tool profile="16.07" id="mothur_merge_sfffiles" name="Merge.sfffiles" version="@WRAPPER_VERSION@.0">
    <description>Merge SFF files</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
#for $i in $input:
    ln -s '$i' input${input.index($i)}.dat &&
#end for

echo 'merge.sfffiles(
    sff=#for $i in $input#input${input.index($i)}.dat-#end for#,
    output=$output
)'
| sed 's/ //g'  ## mothur trips over whitespace
| sed 's/-,/,/g'
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="input" type="data" format="sff" multiple="true" label="input - sff files to merge"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="output" format="sff" label="${tool.name} on ${on_string}: merged sff"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="Fasting_Example1.sff,Fasting_Example2.sff"/>
            <output name="output" ftype="sff">
                <assert_contents>
                    <has_text text="FLP3FBN01ELBSX"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

.. _Mothur: https://www.mothur.org/wiki/Main_Page

**Command Documentation**

The merge.sfffiles_ command merge inputs into a single output.

.. _merge.sfffiles: https://www.mothur.org/wiki/Merge.sfffiles

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