Mercurial > repos > iuc > mothur_summary_qual
diff summary.qual.xml @ 3:30b226ea4888 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:15:04 -0500 |
| parents | c6f0d24c9cfe |
| children | 5ff676aa0986 |
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--- a/summary.qual.xml Tue Sep 05 16:39:52 2017 -0400 +++ b/summary.qual.xml Wed Feb 14 09:15:04 2018 -0500 @@ -7,25 +7,25 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$qfile" qfile.dat && - ln -s "$name" name.dat && - ln -s "$count" count.dat && +## create symlinks to input datasets +ln -s '$qfile' qfile.dat && +ln -s '$name' name.dat && +ln -s '$count' count.dat && - echo 'summary.qual( - qfile=qfile.dat - #if $name: - ,name=name.dat - #end if - #if $count: - ,count=count.dat - #end if - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'summary.qual( + qfile=qfile.dat + #if $name: + ,name=name.dat + #end if + #if $count: + ,count=count.dat + #end if +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/> @@ -43,8 +43,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -53,7 +52,7 @@ The summary.qual_ command reads a quality file and an optional name, and summarizes the quality information. .. _summary.qual: https://www.mothur.org/wiki/Summary.qual -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>