Mercurial > repos > iuc > mothur_merge_sfffiles
view merge.sfffiles.xml @ 0:e7f1da3e0339 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 05:15:22 -0400 |
parents | |
children | e0d980518148 |
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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="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"/> </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> <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>