Mercurial > repos > iuc > mothur_mimarks_attributes
diff mimarks.attributes.xml @ 0:1a45cc9dc7ee draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 05:30:43 -0400 |
parents | |
children | 371a522fc3a1 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mimarks.attributes.xml Fri May 19 05:30:43 2017 -0400 @@ -0,0 +1,54 @@ +<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="stdio"/> + <expand macro="version_command"/> + <command><![CDATA[ + @SHELL_OPTIONS@ + + ## create symlinks to input datasets + ln -s "$biosample_in" biosample_in.dat && + + echo 'mimarks.attributes( + xml=biosample_in.dat + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <param name="biosample_in" type="data" format="xml" label="BioSample attributes xml file"/> + <!-- TODO: add package type options (currently none described in documentation apart from default) + <param name="package" type="select" label="package - select the mimarks package you would like to use"> + <option value="MIMARKS.survey" selected="true">MIMARKS.survey</option> + </param>--> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="source_out" format="txt" from_work_dir="biosample_in*.source" label="${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 Documentation** + +The mimarks.attributes_ Reads bioSample Attributes xml and generates source for make.sra command. + +]]> + </help> + <citations> + <citation type="doi">10.1128/AEM.01541-09</citation> + </citations> +</tool>