Mercurial > repos > iuc > mothur_get_otulabels
diff get.otulabels.xml @ 2:29769fb14cd2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:19:23 -0400 |
| parents | ca0c577f910d |
| children |
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--- a/get.otulabels.xml Tue Sep 05 17:07:56 2017 -0400 +++ b/get.otulabels.xml Tue Mar 20 22:19:23 2018 -0400 @@ -7,36 +7,36 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$infile.otu" infile.otu.dat && - ln -s "$accnos" accnos.dat && +## create symlinks to input datasets +ln -s '$infile.otu' infile.otu.dat && +ln -s '$accnos' accnos.dat && - echo 'get.otulabels( - #if $infile.otu.is_of_type("mothur.cons.taxonomy"): - constaxonomy=infile.otu.dat, - #end if - #if $infile.otu.is_of_type("mothur.otu.corr"): - otucorr=infile.otu.dat, - #end if - #if $infile.otu.is_of_type("mothur.axes"): - corraxes=infile.otu.dat, - #end if - #if $infile.otu.is_of_type("mothur.list"): - list=infile.otu.dat, - #end if - #if $infile.otu.is_of_type("mothur.shared"): - shared=infile.otu.dat, - #end if - #if $infile.intype == "in_shared" and $infile.label: - label=$infile.label, - #end if - accnos=accnos.dat - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'get.otulabels( + #if $infile.otu.is_of_type("mothur.cons.taxonomy"): + constaxonomy=infile.otu.dat, + #end if + #if $infile.otu.is_of_type("mothur.otu.corr"): + otucorr=infile.otu.dat, + #end if + #if $infile.otu.is_of_type("mothur.axes"): + corraxes=infile.otu.dat, + #end if + #if $infile.otu.is_of_type("mothur.list"): + list=infile.otu.dat, + #end if + #if $infile.otu.is_of_type("mothur.shared"): + shared=infile.otu.dat, + #end if + #if $infile.intype == "in_shared" and $infile.label: + label=$infile.label, + #end if + accnos=accnos.dat +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="accnos" type="data" format="mothur.otulabels" label="accnos - otulabels" help="Required"/> @@ -55,6 +55,7 @@ <param name="otu" type="data" format="mothur.cons.taxonomy,mothur.otu.corr,mothur.axes" label="cons.taxonomy/otu.corr/axes file" help="constaxonomy file can be obtained by the running classify.otu tool, otucorr from otu.association tool, and corraxes from corr.axes command"/> </when> </conditional> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -67,6 +68,7 @@ <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> <param name="label" value="0.22"/> <output name="pick_out" md5="1868b58c69f48fe0ae14113d1fc50b33" ftype="mothur.shared"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test> @@ -74,25 +76,25 @@ <param name="accnos" value="amazon.accnos.otulabels"/> <param name="otu" value="amazon.pcoa.axes" ftype="mothur.axes"/> <output name="pick_out" md5="c5f9d1a80b85cce640f25eb89cb67509" ftype="mothur.axes"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** -The get.otulabels_ command selects otu labels from the output from classify.otu_, corr.axes_ and otu.association_. This can be useful especially with subsampled datasets or when groups have been selected. +The get.otulabels command selects otu labels from the output from classify.otu_, corr.axes_ and otu.association_. This can be useful especially with subsampled datasets or when groups have been selected. .. _classify.otu: https://www.mothur.org/wiki/Classify.otu .. _corr.axes: https://www.mothur.org/wiki/Corr.axes .. _otu.association: https://www.mothur.org/wiki/Otu.association v.1.27.0: Added list and shared parameters, updated to Mothur 1.33 -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>