Mercurial > repos > iuc > mothur_make_shared
diff make.shared.xml @ 4:5faa13c51864 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:31:17 -0500 |
| parents | 35e4be39c33d |
| children | 0b282bb8843b |
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--- a/make.shared.xml Tue Sep 05 16:17:40 2017 -0400 +++ b/make.shared.xml Wed Feb 14 09:31:17 2018 -0500 @@ -7,43 +7,43 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$intype.otu" intype_otu.dat && - #if $intype.infile == "otulist": - ln -s "$intype.group" intype_group.dat && - #end if +## create symlinks to input datasets +ln -s '$intype.otu' intype_otu.dat && +#if $intype.infile == "otulist": + ln -s '$intype.group' intype_group.dat && +#end if - echo 'make.shared( - #if $intype.infile == "biom": - biom=intype_otu.dat - #else - #if $intype.group.is_of_type("mothur.groups"): - group=intype_group.dat, - #elif $intype.group.is_of_type("mothur.count_table"): - count=intype_group.dat, - #end if - #if $intype.label: - label=${ str($intype.label).replace(",","-") }, - #end if - #if $intype.groups: - groups=${ str($intype.groups).replace(",","-") }, - #end if - list=intype_otu.dat - #end if - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log && +echo 'make.shared( + #if $intype.infile == "biom": + biom=intype_otu.dat + #else + #if $intype.group.is_of_type("mothur.groups"): + group=intype_group.dat, + #elif $intype.group.is_of_type("mothur.count_table"): + count=intype_group.dat, + #end if + #if $intype.label: + label=${ str($intype.label).replace(",","-") }, + #end if + #if $intype.groups: + groups=${ str($intype.groups).replace(",","-") }, + #end if + list=intype_otu.dat + #end if +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log && - ## move output files to correct destination - mv mothur.*.logfile "$logfile" && - #if $intype.infile == 'otulist' and $intype.groups: - mv intype_otu*.groups "$groupout" - #else - mv intype_otu*.shared "$shared" - #end if +## move output files to correct destination +mv mothur.*.logfile "$logfile" && +#if $intype.infile == 'otulist' and $intype.groups: + mv intype_otu*.groups "$groupout" +#else + mv intype_otu*.shared "$shared" +#end if ]]></command> <inputs> <conditional name="intype"> @@ -106,8 +106,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -121,7 +120,7 @@ .. _shared: https://www.mothur.org/wiki/Shared_file .. _rabund: https://www.mothur.org/wiki/Rabund_file .. _make.shared: https://www.mothur.org/wiki/Make.shared -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>