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merge.sfffiles.xml
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merge.sfffiles.xml
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<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="biotools"/>
<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>