Mercurial > repos > iuc > mothur_summary_qual
diff summary.qual.xml @ 2:a40036faabe8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:12:40 -0400 |
| parents | 41f5224b856b |
| children | 7afd2d352e05 |
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--- a/summary.qual.xml Tue Sep 05 17:13:19 2017 -0400 +++ b/summary.qual.xml Tue Mar 20 22:12:40 2018 -0400 @@ -7,30 +7,31 @@ <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"/> <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/> <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -40,11 +41,11 @@ <test> <param name="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual"/> <output name="out_summary" md5="04de7c9d0f3889d5e121db9d9070c935"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -53,7 +54,7 @@ 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>