Mercurial > repos > iuc > mothur_get_sabund
diff get.sabund.xml @ 2:502c0ba699fb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
---|---|
date | Tue, 20 Mar 2018 22:27:36 -0400 |
parents | 579ffc8e2b4b |
children |
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--- a/get.sabund.xml Tue Sep 05 17:03:32 2017 -0400 +++ b/get.sabund.xml Tue Mar 20 22:27:36 2018 -0400 @@ -7,35 +7,37 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$otu" otu.dat && - ln -s "$count" count.dat && +## create symlinks to input datasets +ln -s '$otu' otu.dat && +ln -s '$count' count.dat && - echo 'get.sabund( - #if $label: - label=${ str($label).replace(",","-") }, - #end if - #if $count: - count=count.dat, - #end if - #if $otu.is_of_type("mothur.list"): - list=otu.dat - #elif $otu.is_of_type("mothur.rabund"): - rabund=otu.dat - #end if - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'get.sabund( + #if $label: + label=${ str($label).replace(",","-") }, + #end if + #if $count: + count=count.dat, + #end if + #if $otu.is_of_type("mothur.list"): + list=otu.dat + #elif $otu.is_of_type("mothur.rabund"): + rabund=otu.dat + #end if +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="otu" type="data" format="mothur.list,mothur.rabund" label="list,rabund - List or Rabund"/> <param name="label" type="select" optional="true" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)"> <expand macro="labeloptions"/> </param> - <param name="count" type="data" format="mothur.count_table" optional="true" help="If your list file contains only the unique sequence names because you ran cluster with a count file, be sure to include the count file."/> + <param name="count" type="data" format="mothur.count_table" optional="true" + help="If your list file contains only the unique sequence names because you ran cluster with a count file, be sure to include the count file."/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -45,17 +47,18 @@ <test><!-- test rabund input --> <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/> <output name="sabund" file="amazon.an.sabund2" ftype="mothur.sabund"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test otu list input --> <param name="otu" value="amazon.an.list" ftype="mothur.list"/> <param name="label" value="0.03,0.05"/> <output name="sabund" file="amazon.an.sabund3" ftype="mothur.sabund"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> - <![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -69,7 +72,6 @@ .. _rabund: https://www.mothur.org/wiki/Rabund_file .. _get.sabund: https://www.mothur.org/wiki/Get.sabund -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>