Mercurial > repos > iuc > mothur_get_coremicrobiome
diff get.coremicrobiome.xml @ 3:5e29cbb2fdef draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 10:09:11 -0500 |
| parents | af8e6f1110b3 |
| children | a6e3c040eb53 |
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--- a/get.coremicrobiome.xml Tue Sep 05 16:15:02 2017 -0400 +++ b/get.coremicrobiome.xml Wed Feb 14 10:09:11 2018 -0500 @@ -7,33 +7,33 @@ <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.coremicrobiome( - #if $otu.is_of_type("mothur.relabund"): - relabund=otu.dat - #elif $otu.is_of_type("mothur.shared"): - shared=otu.dat - #end if - #if $label: - ,label=${ str($label).replace(",","-") } - #end if - #if $groups: - ,groups=${ str($groups).replace(",","-") } - #end if - #if $abundance: - ,abundance=$abundance - #end if - #if $samples: - ,samples=$samples - #end if - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'get.coremicrobiome( + #if $otu.is_of_type("mothur.relabund"): + relabund=otu.dat + #elif $otu.is_of_type("mothur.shared"): + shared=otu.dat + #end if + #if $label: + ,label=${ str($label).replace(",","-") } + #end if + #if $groups: + ,groups=${ str($groups).replace(",","-") } + #end if + #if $abundance: + ,abundance=$abundance + #end if + #if $samples: + ,samples=$samples + #end if +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - OTU Shared or Relabund"/> @@ -84,8 +84,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -97,7 +96,6 @@ v1.27.0: Updated to Mothur 1.33 -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>