Mercurial > repos > iuc > mothur_mimarks_attributes
diff mimarks.attributes.xml @ 3:b708a003d02e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:47:27 -0500 |
| parents | 7de47b23e7f9 |
| children | 443256fa340e |
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--- a/mimarks.attributes.xml Tue Sep 05 16:01:59 2017 -0400 +++ b/mimarks.attributes.xml Wed Feb 14 09:47:27 2018 -0500 @@ -1,4 +1,4 @@ -<tool profile="16.07" id="mothur_mimarks_attributes" name="Get.mimarkspackage" version="@WRAPPER_VERSION@.0"> +<tool profile="16.07" id="mothur_mimarks_attributes" name="Mimarks.attributes" version="@WRAPPER_VERSION@.0"> <description>Reads bioSample Attributes xml and generates source for get.mimarkspackage command</description> <macros> <import>macros.xml</import> @@ -7,17 +7,17 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$biosample_in" biosample_in.dat && +## create symlinks to input datasets +ln -s '$biosample_in' biosample_in.dat && - echo 'mimarks.attributes( - xml=biosample_in.dat - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'mimarks.attributes( + xml=biosample_in.dat +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="biosample_in" type="data" format="xml" label="BioSample attributes xml file"/> @@ -37,17 +37,19 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** -The mimarks.attributes_ Reads bioSample Attributes xml and generates source for make.sra command. +The mimarks.attributes_ command reads `BioSample Attributes`_ xml and generates source for get.mimarkspackage_ command. -]]> - </help> +.. _mimarks.attributes: https://www.mothur.org/w/index.php?search=mimarks.attributes +.. _BioSample Attributes: https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/ +.. _get.mimarkspackage: https://www.mothur.org/wiki/Get.mimarkspackage + + ]]></help> <citations> <citation type="doi">10.1128/AEM.01541-09</citation> </citations>