Mercurial > repos > iuc > mothur_sub_sample
diff sub.sample.xml @ 3:1f5904c5ee42 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 10:11:07 -0500 |
| parents | f18e9f139d14 |
| children | 90c49ac0776e |
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--- a/sub.sample.xml Tue Sep 05 16:15:20 2017 -0400 +++ b/sub.sample.xml Wed Feb 14 10:11:07 2018 -0500 @@ -7,64 +7,64 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$input.otu" input_otu.dat && - ln -s "$count" count.dat && - ln -s "$taxonomy" taxonomy.dat && - #if $input.format == "fasta": - ln -s "$input.name_in" input_name_in.dat && - #end if - #if ($input.format == "fasta" or $input.format == "list") and $input.use_group.to_filter == "yes": - ln -s "$input.use_group.group_in" input_use_group_group_in.dat && - #end if +## create symlinks to input datasets +ln -s '$input.otu' input_otu.dat && +ln -s '$count' count.dat && +ln -s '$taxonomy' taxonomy.dat && +#if $input.format == "fasta": + ln -s '$input.name_in' input_name_in.dat && +#end if +#if ($input.format == "fasta" or $input.format == "list") and $input.use_group.to_filter == "yes": + ln -s '$input.use_group.group_in' input_use_group_group_in.dat && +#end if - echo 'sub.sample( - #if $input.format == "fasta": - fasta=input_otu.dat - #if $input.name_in: - ,name=input_name_in.dat - #end if - #else - #if $input.format == "list": - list=input_otu.dat - #elif $input.format == "sabund": - sabund=input_otu.dat - #elif $input.format == "rabund": - rabund=input_otu.dat - #elif $input.format == "shared": - shared=input_otu.dat - #if $input.groups: - ,groups=${ str($input.groups).replace(",","-") } - #end if - #end if - #if $input.label: - ,label=${ str($input.label).replace(",","-") } - #end if +echo 'sub.sample( + #if $input.format == "fasta": + fasta=input_otu.dat + #if $input.name_in: + ,name=input_name_in.dat + #end if + #else + #if $input.format == "list": + list=input_otu.dat + #elif $input.format == "sabund": + sabund=input_otu.dat + #elif $input.format == "rabund": + rabund=input_otu.dat + #elif $input.format == "shared": + shared=input_otu.dat + #if $input.groups: + ,groups=${ str($input.groups).replace(",","-") } #end if - #if $input.format == "fasta" or $input.format == "list": - #if $input.use_group.to_filter == "yes": - ,group=input_use_group_group_in.dat - #if $input.use_group.groups: - ,groups=${ str($input.use_group.groups).replace(",","-") } - #end if - ,persample=$input.use_group.persample - #end if + #end if + #if $input.label: + ,label=${ str($input.label).replace(",","-") } + #end if + #end if + #if $input.format == "fasta" or $input.format == "list": + #if $input.use_group.to_filter == "yes": + ,group=input_use_group_group_in.dat + #if $input.use_group.groups: + ,groups=${ str($input.use_group.groups).replace(",","-") } #end if - #if $count: - ,count=count.dat - #end if - #if $taxonomy: - ,taxonomy=taxonomy.dat - #end if - #if $size: - ,size=$size - #end if - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log + ,persample=$input.use_group.persample + #end if + #end if + #if $count: + ,count=count.dat + #end if + #if $taxonomy: + ,taxonomy=taxonomy.dat + #end if + #if $size: + ,size=$size + #end if +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <conditional name="input"> @@ -285,8 +285,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -300,7 +299,6 @@ .. _sabund: https://www.mothur.org/wiki/Sabund_file .. _sub.sample: https://www.mothur.org/wiki/Sub.sample -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>