Mercurial > repos > iuc > mothur_get_relabund
diff get.relabund.xml @ 0:4ad3ea2f8584 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 05:46:09 -0400 |
parents | |
children | 47e9c119ac28 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get.relabund.xml Fri May 19 05:46:09 2017 -0400 @@ -0,0 +1,80 @@ +<tool profile="16.07" id="mothur_get_relabund" name="Get.relabund" version="@WRAPPER_VERSION@.0"> + <description>Calculate the relative abundance of each otu</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 "$otu" otu.dat && + + echo 'get.relabund( + shared=otu.dat, + #if $label: + label=${ str($label).replace(",","-") }, + #end if + #if $groups: + groups=${ str($groups).replace(",","-") }, + #end if + scale=$scale + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared" help="Use Make.shared to create a shared file from a list and a group file"/> + <param name="label" type="select" label="label - OTU Labels" multiple="true"> + <expand macro="labeloptions"/> + </param> + <param name="groups" type="select" multiple="true" label="groups - Groups to consider"> + <options> + <filter type="data_meta" ref="otu" key="groups"/> + </options> + </param> + <param name="scale" type="select" label="scale - Scale by"> + <option value="totalgroup" selected="true">Total Groups</option> + <option value="totalotu">Total OTUs</option> + <option value="averagegroup">Average Groups</option> + <option value="averageotu">Average OTUs</option> + </param> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="relabund" format="mothur.relabund" from_work_dir="otu*.relabund" label="${tool.name} on ${on_string}: relabund"/> + </outputs> + <tests> + <test> + <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> + <output name="relabund" file="amazon.an.relabund" ftype="mothur.relabund"/> + <expand macro="logfile-test"/> + </test> + <test> + <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> + <param name="label" value="0.03,0.05,0.22"/> + <param name="groups" value="forest"/> + <output name="relabund" md5="3f91820ebdf2d4c640b7d1489fd67936" ftype="mothur.relabund"/> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The get.relabund_ command calculates the relative abundance of each otu in a sample from a shared_ file. It outputs a .relabund_ file. + +.. _shared: https://www.mothur.org/wiki/Shared_file +.. _get.relabund: https://www.mothur.org/wiki/Get.relabund + +v.1.21.0: Updated to Mothur 1.33 +]]> + </help> + <expand macro="citations"/> +</tool>