Mercurial > repos > iuc > mothur_get_relabund
diff get.relabund.xml @ 3:9bdff4305752 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 10:05:23 -0500 |
| parents | 6495d62d9eb4 |
| children | 97cfb589c26c |
line wrap: on
line diff
--- a/get.relabund.xml Tue Sep 05 16:45:29 2017 -0400 +++ b/get.relabund.xml Wed Feb 14 10:05:23 2018 -0500 @@ -7,27 +7,28 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$otu" otu.dat && +## create symlinks to input datasets +ln -s '$otu' otu.dat && - echo 'get.relabund( - shared=otu.dat, - #if $label: - label=${ str($label).replace(",","-") }, - #end if - #if $groups: - groups=${ str($groups).replace(",","-") }, - #end if - scale=$scale - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log + echo 'get.relabund( + shared=otu.dat, + #if $label: + label=${ str($label).replace(",","-") }, + #end if + #if $groups: + groups=${ str($groups).replace(",","-") }, + #end if + scale=$scale +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> - <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared" help="Use Make.shared to create a shared file from a list and a group file"/> + <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared" + help="Use Make.shared to create a shared file from a list and a group file"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <expand macro="labeloptions"/> </param> @@ -61,8 +62,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -74,7 +74,7 @@ .. _get.relabund: https://www.mothur.org/wiki/Get.relabund v.1.21.0: Updated to Mothur 1.33 -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>