Mercurial > repos > iuc > mothur_get_group
diff get.group.xml @ 0:64172c653a64 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
| author | iuc |
|---|---|
| date | Fri, 24 Jun 2016 16:31:33 -0400 |
| parents | |
| children | 583954d9f36e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get.group.xml Fri Jun 24 16:31:33 2016 -0400 @@ -0,0 +1,53 @@ +<tool profile="16.07" id="mothur_get_group" name="Get.group" version="@WRAPPER_VERSION@.0"> + <description>group names from shared or from list and group</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 "$otu" otu.dat && + + echo 'get.group( + shared=otu.dat + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur && + + ## parse relevant output from logfile to file + cat mothur.*.logfile + | head -n-6 + | sed '1,29d' + > "$bootgroups" + ]]></command> + <inputs> + <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="bootgroups" format="mothur.groups" label="${tool.name} on ${on_string}: bootGroups"/> + </outputs> + <tests> + <test> + <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> + <output name="bootgroups" md5="93b9f7ead2ee04f056e77b5bb94ea0dd"/> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documenation** + +The get.group_ command generate principle components plot data. + +.. _get.group: http://www.mothur.org/wiki/Get.group + +v.1.20.0: Updated to Mothur 1.33 +]]> + </help> + <expand macro="citations"/> +</tool>