Mercurial > repos > iuc > mothur_mimarks_attributes
diff mimarks.attributes.xml @ 0:0d6d694d9d18 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
| author | iuc |
|---|---|
| date | Fri, 24 Jun 2016 16:42:10 -0400 |
| parents | |
| children | 7de47b23e7f9 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mimarks.attributes.xml Fri Jun 24 16:42:10 2016 -0400 @@ -0,0 +1,52 @@ +<tool profile="16.07" id="mothur_mimarks_attributes" name="Get.mimarkspackage" version="@WRAPPER_VERSION@.0"> + <description>Reads bioSample Attributes xml and generates source for get.mimarkspackage command</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="aggressive"><![CDATA[ + ## create symlinks to input datasets + ln -s "$biosample_in" biosample_in.dat && + + echo 'mimarks.attributes( + xml=biosample_in.dat + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + ]]></command> + <inputs> + <param name="biosample_in" type="data" format="xml" label="BioSample attributes xml file"/> + <!-- TODO: add package type options (currently none described in documentation apart from default) + <param name="package" type="select" label="package - select the mimarks package you would like to use"> + <option value="MIMARKS.survey" selected="true">MIMARKS.survey</option> + </param>--> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="source_out" format="txt" from_work_dir="biosample_in*.source" label="${tool.name} on ${on_string}: source"/> + </outputs> + <tests> + <test> + <param name="biosample_in" value="biosample.xml" ftype="xml"/> + <output name="source_out" md5="682288477dd8866465ba475bd0825517" ftype="txt"/> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documenation** + +The mimarks.attributes_ Reads bioSample Attributes xml and generates source for get.mimarkspackage command. + +.. _mimarks.attributes: http://www.mothur.org/wiki/Mimarks.attributes + +]]> + </help> + <citations> + <citation type="doi">10.1128/AEM.01541-09</citation> + </citations> +</tool>